From irisawa@agc.co.jp Mon Feb 26 03:30:46 1996 Received: from ns.agc.co.jp for irisawa@agc.co.jp by www.ccl.net (8.7.1/950822.1) id CAA03999; Mon, 26 Feb 1996 02:36:35 -0500 (EST) Received: by ns.agc.co.jp (8.6.12+2.4W/3.3W9-agcns-Nov2495) id QAA20121 for ; Mon, 26 Feb 1996 16:35:55 +0900 Received: from unknown(202.23.93.35) by ns.agc.co.jp via smap (V1.3) id sma020116; Mon Feb 26 16:35:36 1996 Received: from tornado.agc.co.jp by gw.agc.co.jp (8.6.12+2.4W/3.3W9-agcgw-Apr0695) with ESMTP id QAA16904; Mon, 26 Feb 1996 16:57:21 +0900 Received: from harrier.agc.co.jp (harrier [172.16.1.51]) by tornado.agc.co.jp (8.6.12+2.4W/3.4W2-agcms-Jan2296) with SMTP id QAA21209 for ; Mon, 26 Feb 1996 16:34:38 +0900 Received: from [172.16.1.69] (CMD-Q800) by harrier.agc.co.jp (4.1/SMI-4.1-agclocal-Apr2195) id AA16365; Mon, 26 Feb 96 16:37:30 JST Date: Mon, 26 Feb 96 16:37:29 JST X-Sender: irisawa@harrier.agc.co.jp Message-Id: X-Mailer: Macintosh Eudora Pro Version 2.1.3-Jr1 Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-2022-JP" To: chemistry@www.ccl.net From: irisawa@agc.co.jp (Jun Irisawa) Subject: International Conference this year Hello netters, I would be interested in knowing about "international conference" related t o theoretical chemistry or computational chemistry that will hold this year. Any information about it is very appreciate. Thanks a lot for everybody in advance! +=====================================================+ | Jun Irisawa < irisawa@agc.co.jp> | | Asahi Glass Co.Ltd., Research Center | | Kibangijyutu Group | | 1150 Hazawa-cho Kanagawa-ku | | Yokohama 221 Japan | | Phone: +81-45-334-6021 Fax: +81-45-334-6021 | +=====================================================+ From toukie@zui.unizh.ch Mon Feb 26 04:30:45 1996 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.7.1/950822.1) id DAA04519; Mon, 26 Feb 1996 03:35:51 -0500 (EST) Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA17979; Mon, 26 Feb 96 09:35:36 +0100 X-Nupop-Charset: Swiss Date: Mon, 26 Feb 1996 10:36:23 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <38184.toukie@zui.unizh.ch> To: chemistry@www.ccl.net Subject: Seeking programme users Dear Colleagues; I am interested in corresponding with people who are experienced users of the following computational chemistry programmes: LUDI DOCK CAVITY ENZYMIX Kindly contact me directly at toukie@zui.unizh.ch Thanks in advance. Sincerely, (Dr.) S. Shapiro Zuerich toukie@zui.unizh.ch From toukie@zui.unizh.ch Mon Feb 26 05:01:16 1996 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.7.1/950822.1) id DAA04521; Mon, 26 Feb 1996 03:35:51 -0500 (EST) Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA17989; Mon, 26 Feb 96 09:35:44 +0100 X-Nupop-Charset: Swiss Date: Mon, 26 Feb 1996 10:36:30 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <38190.toukie@zui.unizh.ch> To: chemistry@www.ccl.net Subject: Docking ligands Dear Colleagues; I have recently used a DOS version of the programme GERM [see J. Med. Chem. 37: 2527 ('94)] to generate atomistic minireceptor models of the site of interaction of my compounds of interest. Can anyone recommend software compatible with MS-DOS/Windows or Linux which would enable me to generate a picture of the "optimal" way that one of my molecules might dock into an atomistic minireceptor model? Both my molecules and the minireceptor models are in Sybyl .mol2 format (DOS extension ".mol"), but I should be able to change the format, e.g., using a structural format interconversion programme. I would especially appreciate hearing from people who might have had experi- ence accomplishing such "dockings" using either PCModel, HyperChem, or DGEOM/ DGEOM95. Thanks in advance to all responders. Sincerely, (Dr.) S. Shapiro Zuerich toukie@zui.unizh.ch From Steven.Creve@chem.kuleuven.ac.be Mon Feb 26 06:30:46 1996 Received: from hartree.quantchem.kuleuven.ac.b for Steven.Creve@chem.kuleuven.ac.be by www.ccl.net (8.7.1/950822.1) id GAA05580; Mon, 26 Feb 1996 06:05:50 -0500 (EST) Received: by hartree.quantchem.kuleuven.ac.be id AA38138 (5.67b/IDA-1.5 for Computational Chemistry List ); Mon, 26 Feb 1996 12:03:08 +0100 Date: Mon, 26 Feb 1996 12:03:08 +0100 (NFT) From: Steven Creve X-Sender: steven@hartree To: Computational Chemistry List Subject: CCL:G94:orbitals Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Does anyone know how to visulaize G94 (or G92) orbitals, or electron densities? I would appreciate any comment. Thanks. Steven -------------------------------------------------------------------------- Steven Creve steven.creve@chem.kuleuven.ac.be Labo Quantumchemie steven@hartree.quantchem.kuleuven.ac.be Celestijnenlaan 200F 3001-HEVERLEE tel: (32) (16) 32 73 93 BELGIUM fax: (32) (16) 32 79 92 From katsu@ccyi.ccy.yamaguchi-u.ac.jp Mon Feb 26 07:04:19 1996 Received: from ccyi.ccy.yamaguchi-u.ac.jp for katsu@ccyi.ccy.yamaguchi-u.ac.jp by www.ccl.net (8.7.1/950822.1) id GAA05595; Mon, 26 Feb 1996 06:11:22 -0500 (EST) Received: by ccyi.ccy.yamaguchi-u.ac.jp (5.67+1.6W/6.4J.6-branch2) id AA13611; Mon, 26 Feb 96 20:11:14 JST Date: Mon, 26 Feb 96 20:11:14 JST From: katsu@ccyi.ccy.yamaguchi-u.ac.jp (Tsuyoshi Katsuragi) Message-Id: <9602261111.AA13611@ccyi.ccy.yamaguchi-u.ac.jp> To: chemistry@www.ccl.net Subject: AMBER4 MDANAL Dear CCLers: I am executing MD simulation using AMBER4. And I will caluculate correlation function and spectral density using MDANAL module. When I try getting these plots, I must set some variables below line 6th in the "mdain" file. So I made a "mdain" file as described below, but in this case, I could not execute suitable MDANAL calculation. I could only get the message "CORRELATION LIST NOT SPECIFIED ... NCOR = 0 ..." in "mdaout" file. If anyone know suitable subscription in the "mdain" file, Please tell me them. from here, "mdain" file ------------------------------------------------------- SAMPLE PEPTIDE 1 1 1 1 12 0 1 1 1 2 0.0 0.0 0.0 90.0 8 1 3 1 0 0 1 0.025 1 0 0 2 0 0 1 20 20 20 1 4 4 STOP ------------------------------------------------------- ////////////////////////////////////////////////// Tsuyoshi Katsuragi (male) ----------------------------- Department of Biological Science, Faculty of Agriculture, Yamaguchi University 1677-1, Yoshida, Yamaguchi, 753, Japan E-mail: katsu@ccyi.ccy.yamaguchi-u.ac.jp Tel. 81-0839-22-6111 Ext. 477 ////////////////////////////////////////////////// From hebant@ext.jussieu.fr Mon Feb 26 07:30:48 1996 Received: from shiva.jussieu.fr for hebant@ext.jussieu.fr by www.ccl.net (8.7.1/950822.1) id HAA05918; Mon, 26 Feb 1996 07:20:41 -0500 (EST) Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.7.3/jtpda-5.2) with ESMTP id NAA03908 for ; Mon, 26 Feb 1996 13:20:24 +0100 (MET) Received: from [134.157.11.16] by idf.ext.jussieu.fr (8.6.10/jtpda-4.0) with SMTP; Mon, 26 Feb 1996 13:20:20 +0100 X-Sender: hebant@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 26 Feb 1996 13:18:58 +0100 To: CHEMISTRY@www.ccl.net From: hebant@ext.jussieu.fr (Pascal HEBANT) Subject: BLYP and PW91 Does anyone know references where I can find benchmarks on Becke-Lee-Yang Parr and Perdew-Wang GGAs. I will summarize if there is interest enough. 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 Jeffrey.Gosper@brunel.ac.uk Mon Feb 26 08:02:49 1996 Received: from cook.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.7.1/950822.1) id GAA05723; Mon, 26 Feb 1996 06:47:06 -0500 (EST) Received: from chem-pc-18 (actually chem-pc-18.brunel.ac.uk) by cook.brunel.ac.uk with SMTP (PP); Mon, 26 Feb 1996 11:16:32 +0000 Date: Mon, 26 Feb 1996 11:15:47 GMT From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: SUMMARY: Contouring data To: chemistry@www.ccl.net cc: ca92ccm2@brunel.ac.uk Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear CCL readers, Here is a summary of my recent posting regarding contouring. Thanks for those responding Original posting > > we are interested in producing contour plots within one of our > programs of 3D data points. The data has two independent axes (in a regular > array) and a single dependant axis (i.e. the plot is of 2 geometrical and > 1 energy parameters) > > We would like to know whether there is any good sources of information, > code or alogorithms that would help us. > > Thanks for your help > Jeff Gosper and Conor McMenamin Replies ******************************************** Gnuplot is a plotting package that can create these type of plots and many others. It has the capability to print to many different types of devices, including postscript printers. It's a very versatile package. You can get it at ftp.dartmouth.edu. from: Walter Polkosnik ******************************************** I have had a similar probblem which I have successfully solved with: 1. Sigmaplot for Windows - easy to use, great plots 2. Surfer for Windows - easy to use, even better plots 3. GnuPlot for windows/unix - quick and dirty 4. Tecplot for UNIX - does everything you possibly need, and then some... Andrew Podosenin NYU podosnna@archimedes.nyu.edu ******************************************* Spyglass produces something called "Plot" for PC, mac, SGI, RS/6000 etc. platforms. It is very friendly and produces nice plots in many dimensions. David P. White ****************************************** The freeware program GNUPlot can do surface and contour plots on data similar to that which you describe. It is available on most ftp sites and has a usenet newgroup 'comp.graphics.gnuplot' Cheers, Craig "Never make anything simple and efficient when a way can be found to make it complex and wonderful." Craig Taverner Structural Chemistry, University of the Witwatersrand, South Africa tel: +27-11-716-2290 fax: +27-11-716-3826 email: craig@hobbes.gh.wits.ac.za www: http://www.gh.wits.ac.za/craig **************************************** I've used a couple of different programs to graph contour data. SM (see http://blas.cis.mcmaster.ca/~monger/sm.html ) an easy-to-use script-type interface; produces graphical output on a number of different device types (including PostScript output) IRIS Explorer (see http://www.nag.co.uk:70/Welcome_IEC.html ) Top-notch graphics; worth investing the time to learn how to use it Conrec (see BYTE, 1987 June, p. 143, by Paul D. Bourke) actually, I translated the QuickBASIC source listed into C with the graphics being rendered on a Tcl/Tk canvas; for more info on Tcl/Tk, see http://www.sunlabs.com:80/research/tcl/ I am willing to share this code if you need something to integrate into your own package Check out GNUPlot, too, from the GNU gang. Good Luck! Michael -- Michael A. Peterson peterson@chem.iupui.edu ************************************* Take a look at gnuplot from ftp://prep.ai.mit.edu/pub/gnu. Harry Johnson ************************************* I can recommend the Matlab package for 2D contour or 3D mesh plots, it is also possible two create graphs with both types in the same figure. Matlab is available for the PC and the Macintosh as well as all major Unix workstations, for more info see http://www.mathworks.com/ Johan Landin ************************************ /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://http1.brunel.ac.uk:8080/~castjjg \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From tamasgunda@tigris.klte.hu Mon Feb 26 10:30:48 1996 Received: from tigris.klte.hu for tamasgunda@tigris.klte.hu by www.ccl.net (8.7.1/950822.1) id JAA07759; Mon, 26 Feb 1996 09:47:43 -0500 (EST) Message-Id: <199602261447.JAA07759@www.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Mon, 26 Feb 1996 15:46:27 EST Sender: X-MX-Warning: Warning -- Invalid "From" header. From: "tamasgunda@tigris.klte.hu" To: chemistry@www.ccl.net Date: Mon, 26 Feb 1996 15:27:21 +1 MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Cu complexes Priority: normal X-mailer: Pegasus Mail/Windows (v1.22) Hi Netters, Could you suggest me a few starting literatures on the semiempirical calculations of Cu complexes with amino acids and hydroxamic acids? Kind regads Tamas ************************************************************************ Tamas E. Gunda, Ph.D. phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 H-4010 Debrecen Hungary ************************************************************************ From carlos@penelope.bio.cornell.edu Mon Feb 26 10:40:18 1996 Received: from CORNELLC.cit.cornell.edu for carlos@penelope.bio.cornell.edu by www.ccl.net (8.7.1/950822.1) id JAA07803; Mon, 26 Feb 1996 09:53:25 -0500 (EST) Received: from penelope.bio.cornell.edu by CORNELLC.cit.cornell.edu (IBM VM SMTP V2R3) with TCP; Mon, 26 Feb 96 09:53:06 EST Received: by penelope.bio.cornell.edu (940816.SGI.8.6.9/921111.SGI) for chemistry@www.ccl.net id JAA10487; Mon, 26 Feb 1996 09:41:56 -0500 Date: Mon, 26 Feb 1996 09:41:56 -0500 From: carlos@penelope.bio.cornell.edu (Carlos Faerman) Message-Id: <199602261441.JAA10487@penelope.bio.cornell.edu> To: chemistry@www.ccl.net Subject: Neural networks and structural biology I would like to pose the following question: What is the success rate of neural networks when applied to predictions of structural motifs? I would like to know what is the experience so far. Please reply directly to me, and if there is enough interest, I will summarize the answers Thanks CHF ********************************************** * Dr. Carlos H. Faerman * * Biochemistry, Molecular and Cell Biology * * Cornell University * * 221 Biotechnology Building * * Ithaca, NY 14853 * * USA * * ........................................ * * carlos@penelope.bio.cornell.edu * * Phone: (607)255-8432 * ********************************************** From c.s.page@ic.ac.uk Mon Feb 26 11:30:49 1996 Received: from punch.ic.ac.uk for c.s.page@ic.ac.uk by www.ccl.net (8.7.1/950822.1) id KAA08595; Mon, 26 Feb 1996 10:58:27 -0500 (EST) Received: from judy.ic.ac.uk by punch.ic.ac.uk with SMTP (PP); Mon, 26 Feb 1996 15:06:49 +0000 Received: from chcmga.ch.ic.ac.uk (chcmga.ch.ic.ac.uk [155.198.232.23]) by judy.ic.ac.uk (8.7.4/8.7.4) with SMTP id PAA28513; Mon, 26 Feb 1996 15:06:08 GMT Received: from titanium by chcmga.ch.ic.ac.uk (940816.SGI.8.6.9/4.0) id PAA10159; Mon, 26 Feb 1996 15:06:07 GMT Date: Mon, 26 Feb 1996 15:06:06 +0000 (gmt) From: "Mr C. S. Page" To: Steven Creve cc: Computational Chemistry List Subject: Re: CCL:G:G94:orbitals In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 26 Feb 1996, Steven Creve wrote: > Does anyone know how to visulaize G94 (or G92) orbitals, or electron > densities? I would appreciate any comment. We have a module that runs within SGI IRIS Explorer to read and display G94 cube files of all types. Please contact either myself or Omer Casher (o.casher@ic.ac.uk) for details. If there is sufficient interest, we shall make the executable available from our Web site. Chris Page __________ Department of Chemistry Tel: +44 (0)171 594 5795 Imperial College GB-LONDON SW7 2AY From uucp@scnit.saratov.su Mon Feb 26 12:30:50 1996 Received: from sovcom.kiae.su for uucp@scnit.saratov.su by www.ccl.net (8.7.1/950822.1) id MAA08933; Mon, 26 Feb 1996 12:02:17 -0500 (EST) Received: by sovcom.kiae.su id AA15726 (5.65.kiae-1 for chemistry@www.ccl.net); Mon, 26 Feb 1996 19:49:07 +0300 Received: by sovcom.KIAE.su (UUMAIL/2.0); Mon, 26 Feb 96 19:49:07 +0300 Received: by scnit.saratov.su (UUPC/@ v6.14d, 30Mar95); id AA25615 Mon, 26 Feb 1996 11:56:52 +0300 To: chemistry@www.ccl.net Message-Id: Organization: Saratov State University From: "pankratov" Date: Mon, 26 Feb 96 11:56:50 +0300 X-Mailer: BML [MS/DOS Beauty Mail v1.36h] Subject: MOPAC Spin Density Matrix Interpretation Lines: 18 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear netters, I would greatly appreciate an advice concerning interpretation of the UHF MOPAC spin density matrix. To obtain spin densities on atoms, is it correct to summarize the diagonal elements? What is the physical sense of the non-diagonal elements, which are absent within the more simple consideration, e.g., for the RHF (INDO or others), where spin density is equal to "ro alpha" minus "ro beta"? Prof. Dr. Sc. Alexei N. Pankratov Department of Chemistry N.G. Chernyshevskii Saratov State University 83 Astrakhanskaya Str., Saratov 410071 Russia E-mail: pankratov@scnit.saratov.su Fax: ++7(8452)240446 From owner-chemistry@ccl.net Mon Feb 26 13:30:51 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id MAA09152; Mon, 26 Feb 1996 12:31:52 -0500 (EST) Received: from copland.udel.edu for sbennett@wotan.duch.udel.edu by bedrock.ccl.net (8.7.1/950822.1) id MAA26083; Mon, 26 Feb 1996 12:31:48 -0500 (EST) Received: from wotan.duch.udel.edu (wotan.duch.udel.edu [128.175.54.25]) by copland.udel.edu (8.6.12/8.6.12) with ESMTP id MAA12268 for <@brahms.udel.edu:chemistry@ccl.net>; Mon, 26 Feb 1996 12:31:32 -0500 Received: by wotan.duch.udel.edu (940816.SGI.8.6.9/930416.SGI) id MAA00763; Mon, 26 Feb 1996 12:30:59 -0500 Date: Mon, 26 Feb 1996 12:30:59 -0500 (EST) From: Steve Bennett To: CCL Users Subject: GNU plot for the Power Mac Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone know if gnu plot has been compiled for the PowerMac? Or if there are CodeWarrior projects available for the source code? Thanks in advance. Steven D. Bennett University of Delaware Department of Chemistry 304A Drake Hall (302) 831-8720 sbennett@wotan.duch.udel.edu (302) 737-8485 http://www.udel.edu/arcade/steves.html "Although the answer is not unknown, I'm searchin', searchin, and how I've grown; It's not all right to say goodbye, and the world on a string doesn't mean a thing" Neil Young From jkl@ccl.net Mon Feb 26 13:35:43 1996 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.7.1/950822.1) id NAA10070; Mon, 26 Feb 1996 13:26:23 -0500 (EST) Received: from krakow.ccl.net for jkl@ccl.net by bedrock.ccl.net (8.7.1/950822.1) id NAA27268; Mon, 26 Feb 1996 13:26:21 -0500 (EST) From: Jan Labanowski Received: for jkl@ccl.net by krakow.ccl.net (8.6.10/920428.1525) id NAA00865; Mon, 26 Feb 1996 13:26:20 -0500 Date: Mon, 26 Feb 1996 13:26:20 -0500 Message-Id: <199602261826.NAA00865@krakow.ccl.net> To: chemistry@www.ccl.net Subject: Lead Generation and Optimization - Wrksp Forwarding: Mail from 'cjohnson@ccl.net (Cheryl Johnson)' dated: Mon, 26 Feb 1996 11:33:52 -0500 (EST) Cc: jkl@ccl.net, cjohnson@ccl.net Lead Generation and Optimization March 21-22, 1996 Sheraton New Orleans Hotel New Orleans, Louisana Contact/Organizer: Mark Alexay, Straegic Research Institute 212-302-1800, x251 Theme: "Exploiting Drug Discovery Resources for Maximum Yield" Topics Include: -- Combinatorial Chemistry -- High-Throughput Screening -- Natural Products Screening -- 2D and 3D Chemical Databases -- Measurement of Chemical Diversity -- De Novo Drug Design -- Peptidomimetic Design -- 2D and 3D QSAR -- Structure-based Design -- Models of Oral Bioavailability -- X-Ray Crystallography -- Solid Phase Chemistry -- Pharmacophore Mapping -- Flexible Docking Conference Chairman: Alan Katz, Ph.D. Research Fellow, Structural Biology Dept. of Computational Chemistry Wyeth-Ayerst Research Conference Co-Chairman: Frank K. Brown, Ph.D. Section Head, Chemoinformatics Glaxo-Wellcome, Inc. UPDATE on participation: Among your collegues attending the March 21-22, 1996 conference are representatives from this growing list of companies and universities: - Proctor and Gamble - Sandoz Research Institute - Searle - Abbott Laboratories - XOMA Corporation - Astra Arcus - Xavier University - Pfizer - American Cyanamid - Dupont Merck - SmithKline Beecham - Akzo Nobel - Eli Lilly & Co. - National Institute of Health - Hoechst AG - Ciba Geigy - Roche Biosciences - COR Therapeutics - SIBIA - Rhone Poulenc Rorer - Bristol Myers Squibb - Johnson & Johnson PRI - Hoechst Marion Roussel - Pharmacia Upjohn - Sagami Chemical - Guilford dPharmaceuticals - Ono Pharmaceuticals - Cubist, Inc. - Specs and Biospecs - Nexstar Pharmaceuticals - Cambridge Neuroscience From jxh@ibm12.biosym.com Mon Feb 26 15:30:50 1996 Received: from bioc1.biosym.com for jxh@ibm12.biosym.com by www.ccl.net (8.7.1/950822.1) id OAA10645; Mon, 26 Feb 1996 14:41:43 -0500 (EST) Received: from ibm12.biosym.com by bioc1.biosym.com (5.64/0.0) id AA02628; Mon, 26 Feb 96 11:45:45 -0800 Received: by ibm12.biosym.com (AIX 3.2/UCB 5.64/4.03) id AA21443; Mon, 26 Feb 1996 11:39:18 -0800 Received: from Messages.8.5.N.CUILIB.3.45.SNAP.NOT.LINKED.ibm12.biosym.com.rs.aix3 via MS.5.6.ibm12.biosym.com.rs_aix3; Mon, 26 Feb 1996 11:39:18 -0800 (PST) Message-Id: Date: Mon, 26 Feb 1996 11:39:18 -0800 (PST) From: Joerg Hill X-Andrew-Message-Size: 2179+0 Mime-Version: 1.0 Content-Type: text/richtext; charset=US-ASCII Content-Transfer-Encoding: quoted-printable To: CHEMISTRY@www.ccl.net Subject: Re: CCL:BIG AB INITIO JOBS Since there seems to be some interest in large ab initio jobs I thought I contribute the following: Complete geometry optimizations: Compound Symmetry # of basis functions 1,6-di-Al-octahydroxyoctasilsesquioxane Ci 614 1,3,5,7-tetra-Al-octahydroxyoctasilsesquioxane C2 624 Dodecahydroxydodecasilsesquioxane D6h 906 1,9-di-Al-dodecahydroxydodecasilsesquioxane C2h 916 Sodalite cage Oh 1812 (J.-R. Hill and J.Sauer: J. Phys. Chem. 98, (1994), 1238 and 99, (1995), 9536) Complete geometry optimization and NMR-chemical shifts: Octahydroxyoctasilsesquioxane anion C1 648 (J. Sauer and J.-R. Hill: Chem. Phys. Letters, 218 (1994), 333) I did calculation of that size pretty routinely a few years ago. All these calculations have been done using IBM RS/6000 single work- stations or clusters of up to five of them. The programme used was in all cases Turbomole which makes pretty good use of symmetry. Joerg-R. Hill ----------------------------------------------------------------------------= ---- Dr. Joerg-Ruediger Hill | Every attempt to employ mathematical methods in the Biosym/MSI | study of chemical questions must be considered pro- 9685 Scranton Road | foundly irrational and contrary to the spirit of San Diego, CA 92121-2777 | chemistry ... If mathematical analysis should ever USA | hold a prominent place in chemistry - an aberration | which is happily almost impossible - it would Phone (619) 546-5508 | occasion a rapid and widespread degeneration of Fax (619) 458-0136 | that science. E-mail jxh@biosym.com | Auguste Comte, Philosophie Positive, Paris, 1838 ----------------------------------------------------------------------------= ---- The opinions expressed in this message are my personal opinions and no offical statements of Biosym Technologies, Inc. For informations about Biosym products take a look at: http://www.biosym.com/. ----------------------------------------------------------------------------= ---- From ZAHAREVITZ@dtpax2.ncifcrf.gov Mon Feb 26 16:04:05 1996 Received: from dtpax2.ncifcrf.gov for ZAHAREVITZ@dtpax2.ncifcrf.gov by www.ccl.net (8.7.1/950822.1) id PAA10938; Mon, 26 Feb 1996 15:39:57 -0500 (EST) Date: Mon, 26 Feb 1996 15:38:05 -0500 (EST) From: Dan Zaharevitz 301-496-8747 To: chemistry@www.ccl.net CC: ZAHAREVITZ@dtpax2.ncifcrf.gov Message-Id: <960226153805.20220d4a@dtpax2.ncifcrf.gov> Subject: Structural and biological data available from NCI The Developmental Therapeutics Program, Division of Cancer Treatment, Diagnosis, and Centers, National Cancer Institute runs a major screening program for the testing of compounds for anti-cancer and anti-AIDS activity. A large part of the data generated by these screens is now available via the DTP's WWW page. The URL: http://epnws1.ncifcrf.gov:2345/dis3d/dtp.html Screening results for over 20,000 compounds that have been tested in the human tumor cell line screen are available in a compressed comma delimited file ( and also in a series of text files). Structural data for these compounds is provided in the form of a compressed file in MDL SDFile format. Screening results are also available for over 25,000 compounds tested in the AIDS antiviral screen. Again biological results are in a text file and structural data in a compressed file in MDL SDFile format. Connection tables for about 125,000 compounds are also available. These are the same set of compounds that many software companies have made available. Prof. Gasteiger's group has used their program Corina to convert this set to 3D structures and these structures are also available. There is at least one company that is selling this set of 3D structures. The NCI has no connection with this or any other sale of this data. It is up to each individual to decide whether what they are buying is worth the price. The data described above is only available in bulk format, no tools are provided for searching for a particular subset of interest. There are, however, a few hundred compounds of special interest that are searchable by NSC number (the NCI's internal ID number) and by compound name. We are working on providing search capability for the larger set of data, but do not yet have a good estimate of when that might be available. There are also pages that provide explanation and technical details for these screens and current methods of analysis. The DTP is committed to making these pages as useful as possible to as many people as possible. Improvement is very much dependent on user feedback. Any problems, corrections, suggestions, etc. should be emailed to: zaharevitz@dtpax2.ncifcrf.gov /********************************************************************** * Dan Zaharevitz * Information Technology Branch, Developmental Therapeutics Program * National Cancer Institute * EPN Room 811, 6130 Executive Blvd. Rockville, MD 20892-9903 * email: zaharevitz@dtpax2.ncifcrf.gov **********************************************************************/ From mecolv@california.sandia.gov Mon Feb 26 17:30:51 1996 Received: from california.sandia.gov for mecolv@california.sandia.gov by www.ccl.net (8.7.1/950822.1) id RAA12218; Mon, 26 Feb 1996 17:29:07 -0500 (EST) Received: (from mecolv@localhost) by california.sandia.gov (8.7.3/1.15) id OAA09093; Mon, 26 Feb 1996 14:29:03 -0800 Date: Mon, 26 Feb 1996 14:29:03 -0800 From: mecolv@california.sandia.gov (colvin michael e) Message-Id: <199602262229.OAA09093@california.sandia.gov> To: chemistry@www.ccl.net In-reply-to: <9602240946.AA17535@risc1.lrm.fi.cnr.it> (thep@risc1.lrm.fi.cnr.it) Subject: Re: CCL:calculate the angle Recently thep@risc1.lrm.fi.cnr.it (Pornthep Sompornpisut) asked: >I will appreciate if anyone know of any programs that can measure the angle >between the planes? You are probably looking for something that has a nice GUI for selecting the atoms, but if you just want a program to calculate the angles, here's a tiny C code I wrote sometime back to do this. It just reads sets of six cartesian points, three each per plane, and prints out the angle. Nota bene: To the best of my knowledge it works, but of course I offer no guarantees to its accuracy, reliability, suitability, etc. etc..., so definitely check this against a hand-calculated result. --Mike Colvin mecolv@ca.sandia.gov ============================================================= /* Routine to calculate the angle between two planes */ #include #include typedef struct { double x; double y; double z; } point; int main(void); point cross(point, point); double dot(point, point); main() { point a1,a2,a3,b1,b2,b3; point va1,va2,vb1,vb2, crossa, crossb; double dotab, angle; while(1) { if (scanf("%lf %lf %lf",&a1.x,&a1.y,&a1.z)==EOF) exit(0); scanf("%lf %lf %lf",&a2.x,&a2.y,&a2.z); scanf("%lf %lf %lf",&a3.x,&a3.y,&a3.z); scanf("%lf %lf %lf",&b1.x,&b1.y,&b1.z); scanf("%lf %lf %lf",&b2.x,&b2.y,&b2.z); scanf("%lf %lf %lf",&b3.x,&b3.y,&b3.z); /* calculate direction vectors */ va1.x=a2.x-a1.x; va1.y=a2.y-a1.y; va1.z=a2.z-a1.z; va2.x=a3.x-a1.x; va2.y=a3.y-a1.y; va2.z=a3.z-a1.z; vb1.x=b2.x-b1.x; vb1.y=b2.y-b1.y; vb1.z=b2.z-b1.z; vb2.x=b3.x-b1.x; vb2.y=b3.y-b1.y; vb2.z=b3.z-b1.z; /* calculate cross products */ crossa=cross(va1,va2); crossb=cross(vb1,vb2); dotab=dot(crossa,crossb); dotab/=sqrt(dot(crossa,crossa)); dotab/=sqrt(dot(crossb,crossb)); angle=acos(dotab)*180/3.1415926535; printf(" Angle = %lf\n",angle); } } point cross(point a, point b) { point value; value.x=a.y*b.z-a.z*b.y; value.y=a.z*b.x-a.x*b.z; value.z=a.x*b.y-a.y*b.x; return value; } double dot(point a, point b) { return a.x*b.x+a.y*b.y+a.z*b.z; } ============================================================= From albeiro@chem.cmu.edu Sat Feb 24 13:54 EST 1996 Received: from chopin.chem.cmu.edu for albeiro@chem.cmu.edu by www.ccl.net (8.7.1/950822.1) id NAA20680; Sat, 24 Feb 1996 13:54:34 -0500 (EST) Received: from polaron.chem.cmu.edu (POLARON.CHEM.CMU.EDU [128.2.43.16]) by chopin.chem.cmu.edu (8.6.4/8.6.4) with ESMTP id NAA01872; Sat, 24 Feb 1996 13:54:33 -0500 Received: from localhost (localhost [127.0.0.1]) by polaron.chem.cmu.edu (8.6.4/8.6.4) with SMTP id NAA13645; Sat, 24 Feb 1996 13:54:33 -0500 From: Albeiro Alonso Restrepo Cossio Message-Id: <199602241854.NAA13645@polaron.chem.cmu.edu> X-Authentication-Warning: polaron.chem.cmu.edu: Host localhost didn't use HELO protocol To: chemistry@www.ccl.net cc: albeiro@chopin.chem.cmu.edu Subject: CCL: Summary, Trivial question Date: Sat, 24 Feb 96 13:54:32 -0500 X-Mts: smtp Content-Type: text Content-Length: 10620 Status: RO Dear CCL subscribers, Many thanks to all of you who spent some of your time in answering my question about the biggest system optimized ab initio methodologies ad the biggest water cluster optimized with simulated annealing; here is my summary. Albeiro Restrepo. ******************************************************************************** From: cachau@fcindy5.NCIFCRF.GOV (cachau) Hola Albeiro, Vi tu pregunta en el CCL y me arriesgo a darte mi opinion. Creo que tendras serias dificultades en encontrar una respuesta a tu pregunta. La razon es que necesitas una definicion operativa de "mas grande". Si te fijas en "numero de atomos" puedes elejir una pequenya base y de este modo puedes calcular moleculas muy grandes. Si en cambio prefieres usar como parametro el numero de bases, entonces te encuentras con que hay sistemas diatomicos que se han tratado con muchos cientos de bases y con bases de simetria mas alta que g lo que es inconcebible de usar para una molecula de interes biologico, de modo que siguiendo este criterio llegarias a la conclusion de que una molecula diatomica con algun atomo pesado seria tal vez el sistema mas grande nunca tratado a nivel HF. Entonces, ni el numero de bases ni el numero de atomos constituyen tu definicion. Por si esto no fuera ya complejo, luego tienes que incorporar el problema de optimizacion: HF sin optimizar es un problema, optimizada la estructura es un orden de magnitud mas grande como problema, y si llegas a caracterizar la geometria (calcular su Hessiano) es un orden de magnitud mas alto aun. En la complejidad del problema, como incluyes la simetria?. Hay ENORMES complejos con piridinas resueltos con bases enormes pero con simetria altisima. Que "tamanyo" le asignarias al complejo?. Que tan grande te resulta un buckyball?. 60 atomos o 5 + simetria?. Y luego tienes los calculos 'a la Clementi (posiblemente en mi criterio los mas grandes nunca hechos en biomoleculas) en su famoso "Star" system. El usaba bases muy grandes, pero usaba una "base asociada" a largas distancias de modo que se ahorraba de calcular un numero altisimo de integrales de este modo, como medirias la complejidad en este caso?. En fin, que no te he resuelto tu pregunta, sorry, pero creo que necesitas darle una pulida a tu definicion si quieres que la respuesta sea "meaningful". ******************************************************************************** From: Kris Van Alsenoy Dear Albeiro, In response to your question concerning molecular clusters, I would like to mention the following papers : Anik Peeters, C. van Alsenoy, A.T.H. lenstra, H.J. Geise, Int. J. Quant. Chem., Vol. 46, 73-80 (1993) C. Van Alsenoy, Anik Peeters, J. Mol. Struct., Vol. 286, 19-34 (1993) Anik Peeters, C. Van Alsenoy, A.T.H. Lenstra, H.J. Geise, J. Mol. Strcut., Vol. 304, 101-107 (1994) Anik Peeters, C, Van Alsenoy, A.T.H. Lenstra, H.J. Geise, J. Chem. Phys., Vol. 103, 6608-6616 (1995) In thes epapers we studied a number of molecules using a cluster approach. Is this what you were looking for ? Sincely, kris van alsenoy alsenoy@uia.ua.ac.be ******************************************************************************** From: "E. Lewars" Albeiro Restrepo asked about the biggest systems that have been studied by ab initio, and the reliability of the results. I don't claim that these are the biggest anyone has looked at, but they are at the high end of ab initio jobs: (1) MP2(FC)/6-311G** (312 basis funtions) on C6H5-C:::C-C6H5: S. Saebo and J. Almlof et al, THEOCHEM 59, 361 (1989). (2) MP2/6-31G* optimizations on porphyrins, ca 20 heavy atoms. At the MP2 level, unlike the HF, the known, dampened bond alternation characteristic of these aromatic systems is evident. _Long_ calc's. See L. Paquette et al, ca. 1995 (J Am Chem Soc?). (3) For a short, very useful review of work on ab initio etc calc's and their reliability, see I. N. Levine, _Quantum Chemistry_, 4th Ed., Prentice Hall, 1991, Chapters 15, 16, 17. Errol Lewars ******************************************************************************** From: Artem Masunov Dear Albeiro Restrepo, We did HF optimization of some supermolecular clusters containing up to 80 atoms. They are not published yet. If you find bigger system being optimized, please let me know. Regards, Artem > Does someone in the list have information about the bigest system succesfully > optimized by any ab initio methodology and about its reliability? __ _________ / \ / _ _ \ Artem Masunov - amasunov@shiva.hunter.cuny.edu / \\ \\ \\ \ Chemistry Department, Hunter College / /\ \\ \\ \\ \ City University of New York / ____ \\ \\ \\ \ 695 Park Avenue, New York, NY 10021 /__/\__/\__\\__\\__\\__\ Tel: (212) 725-0317, Fax: (212) 772-5332 \__\/ \/__//__//__//__/ I know you believe you understand what you think I said, but I am not sure you realize that what you heard is not what I meant. (Gaussian92) ******************************************************************************** From: Artem Masunov On Mon, 19 Feb 1996, Albeiro Alonso Restrepo Cossio wrote: > Does your group have any intention of publishing that results? Yes, mixed hexamer of melamine-barbituric acid will be reported on ACS meeting this spring, urea decamers were reported on ACA meeting last summer (see abstract on WWW): http://www.cisti.nrc.ca/programs/ACA95/M/a429.html Papers will be submitted to one of ACS journals in a few month. Regards, Artem ******************************************************************************** From: "Dr. James Brown" On Feb 19, 12:17pm, E. Lewars wrote: > Subject: CCL:BIG AB INITIO JOBS > (1) MP2(FC)/6-311G** (312 basis funtions) on C6H5-C:::C-C6H5: S. Saebo and > J. Almlof et al, THEOCHEM 59, 361 (1989). A study of glucose by us in JACS coming out soon had 348 basis functions. Another on glucose conformers by Truhlar and coworkers to be published in Carbohydrate Research included 624 basis functions. As far as reliability...it's difficult to tell since there's not much data on glucose in the gas phase. James ******************************************************************************** From: Artem Masunov Dear Albeiro Restrepo, Since CCLers started to count basis functions, I can tell, that urea decamer had 840 basis functions (D95**). Mixed hexamer had 918 basis functions (D95*) and will be presented at Symposium Semiempirical methods: Do they have a future? in New Orlean (March 1996) by Prof. J.J.Dannenberg. Artem ******************************************************************************** From: Kris Van Alsenoy Dear Albeiro, I forgot to mention a study on sugars using TZV & TZVP -basisets : C. Van Alsenoy, A.D. French, M. Cao, S.Q. Newton, L. Sch"afer, JACS, Vol. 116, 9590-9595 (1994) sincerly, kris On Mon, 19 Feb 1996, Albeiro Alonso Restrepo Cossio wrote: ******************************************************************************** From: jmuilu@joyke7.joensuu.fi (Juha Muilu) Hi, I have done some ab initio calculations on ZnS clusters up to Zn240S240 (1200 basis functions & 6000 primitive functions). The calculations are made possible using translational properties of finite clusters. What comes to reliability I must say that the models are rather academic.... For more information: http://www.chem.joensuu.fi/people/juha_muilu/Research/zns_clusters.html Also from Surf.Science during this year, I hope. ---- Juha Muilu Department of Chemistry,University of Joensuu,P.O. Box 111 80101 Joensuu,FINLAND/Email:Juha.Muilu@joensuu.fi,Phone:358-73-1513312, Fax:358-73-1513390,http://www.chem.joensuu.fi/people/juha_muilu ******************************************************************************** From: Stuart Watson Hi, Our current record is performing molecular dynamics on 6700 Na atoms, using an "Order-N" DFT method (for the initial article see M. Pearson et al, J. Phys. Cond. Matter, 5, 3321 (1993). The method is only really applicable to systems with delocalised electrons (ie metals), and reproduces Kohn-Sham results for alkali metals. This system was run on a Cray T3D (timing on 128nodes 9s electronic, 1200 ionic - thats the benefit of an Order-N method), and it is feasible to probably quadruple the no. of atoms (as the memory requirements, as well as the time scales linearly). Stuart Watson ########################################################################## # Stuart Watson # Life is like a box of chocolates, # # stuart@physchem.ox.ac.uk # it gets all squishy when dropped # # http://physchem.ox.ac.uk/~stuart # from a great height. # ########################################################################## ******************************************************************************** From: Bryan Marten Zhang and Friesner recently reported Self Consistent Reaction Field (QM solute surrounded by continuum dielectric solvent requiring several converged HF wavefunctions) calculations at the HF/6-31G** level for bacteriochlorophyll and bacteriopheophytin on an IBM RS/6000 workstation using the electronic structure program PSGVB in JPC 99 16479 1995. Those were in the 880-890 basis function range on molecules with C1 (no) symmetry and are believed to be the largest SCRF ab inito calculations to date. The authors use the SCRF calculations to compute redox potentials in DMF, compare to experiment, and report qualitative agreement for relative redox energies. -- Dr. Bryan Marten Ciba Pharmaceuticals martebr2@ussu.ciba.com ******************************************************************************** From: "Schiffer, Heinz, Dr." Sometime ago someone asked for references to large ab initio calculations ( sorry, but I forgot who it was ). I just got a copy of a paper of Gustavo Scuseria at Rice University in Houston who did a Hartree-Fock geometry optimization within icosahedral symmetry for a fullerene with 540 atoms and with 2700 basis functions on a single IBM RS6000 workstation. The program he used was TURBOMOLE from Ahlrichs' group in Karlsruhe. ******************************************************************************** From jankazim@aquila.ichp.waw.pl Mon Feb 26 05:07 EST 1996 Received: from aquila.ichp.waw.pl for jankazim@aquila.ichp.waw.pl by www.ccl.net (8.7.1/950822.1) id FAA05204; Mon, 26 Feb 1996 05:07:28 -0500 (EST) Received: by aquila.ichp.waw.pl (5.65/1.2-eef) id AA26443; Mon, 26 Feb 96 11:04:29 +0100 Date: Mon, 26 Feb 1996 11:04:27 +0100 (CET) From: Jan Kazimirski To: chemistry@www.ccl.net Subject: Question: calc. of PED (potential energy distrib.) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 556 Status: RO Dear Netters One of my friends (not subscribed to CCL - yet(:-()) asked me to send his question to the list. The question is: "Can you recommend any program (commercial or academic) which calculates PED (potential energy distribution) based on Gaussian 94 - calculated vibrational normal modes?" We both (me and my friend) would be grateful for any information. Thanks in advance. Jan Kazimirski e-mail: jankazim@aquila.ichp.waw.pl From osawa@cochem.tutkie.tut.ac.jp Mon Feb 26 18:06 EST 1996 Received: from cochem2.cochem2.tutkie.tut.ac.jp for osawa@cochem.tutkie.tut.ac.jp by www.ccl.net (8.7.1/950822.1) id SAA12752; Mon, 26 Feb 1996 18:06:40 -0500 (EST) Received: from [133.15.160.31] (cochem3.tutkie.tut.ac.jp [133.15.160.31]) by cochem2.cochem2.tutkie.tut.ac.jp (8.6.12+2.4W/3.3W9) with SMTP id IAA22913 for ; Tue, 27 Feb 1996 08:10:08 +0900 Message-Id: <199602262310.IAA22913@cochem2.cochem2.tutkie.tut.ac.jp> Date: Tue, 27 Feb 1996 08:06:11 +0900 To: chemistry@www.ccl.net From: osawa@cochem.tutkie.tut.ac.jp (Eiji Osawa) X-Sender: osawa@cochem2.cochem2.tutkie.tut.ac.jp Subject: WATOC96 2nd circular Return-Receipt-To: osawa@cochem.tutkie.tut.ac.jp MIME-Version: 1.0 X-Mailer: Eudora-J(1.3.8-J13) Content-Type: text/plain; charset=iso-2022-jp Content-Length: 751 Status: R To the list members of Japan, Taiwan, Korea, China and other Asian countries: I have a stock of the 2nd circular for WATOC96, World Congress of Comutational Chemists, to be held in Jerusalem, Israel, July 7 to 12, 1996. Deadline of abstract is April 15, 1996. Those who are interested should send me e-mail for a copy or take a look at its homepage, http://www.ch.ic.ac.uk/watoc/watoc_israel.html. Eiji Osawa /************************************************* * Eiji Osawa * Department of Knowledge-based Information Engineering * Toyohashi University of Technology * Aichi 441, Japan * Phone: x-81-532-47-0111(ex. 853) * FAX: x-81-532-48-5588 * E-mail: osawa@cochem.tutkie.tut.ac.jp *************************************************/ From polowin@hyper.hyper.com Fri Feb 23 11:38 EST 1996 Received: from www.hyper.com for polowin@hyper.hyper.com by www.ccl.net (8.7.1/950822.1) id LAA11892; Fri, 23 Feb 1996 11:38:02 -0500 (EST) Received: from hyper.hyper.com (hyper.hyper.com [204.50.97.9]) by www.hyper.com (8.6.12/8.6.12) with SMTP id LAA19836; Fri, 23 Feb 1996 11:50:43 -0500 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:chemistry@www.ccl.net id AA29565; Fri, 23 Feb 96 11:50:38 -0500 Date: Fri, 23 Feb 96 11:50:38 -0500 From: polowin@hyper.hyper.com (Joel Polowin) Message-Id: <9602231650.AA29565@hyper.hyper.com> To: SUBRAPS@texaco.com, chemistry@www.ccl.net Subject: Re: CCL:Dipole-Dipole Interaction in Dynamics Content-Type: text Content-Length: 885 Status: RO > Date: 21 Feb 1996 07:18:07 GMT > From: SUBRAPS@texaco.com > > Is there a Molecular Dynamics Package which incorporates dipole-dipole > interaction in the electrostatic computation?. > I would appreciate any input in this regard. Any package that does molecular dynamics with an MM2-derived force field should include interactions of bond dipoles. (HyperChem does; please contact me for details.) I don't know of any that explicitly include effects of molecular dipoles, but I'm not sure if that's what you were asking about. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ From SUBRAPS@texaco.com Mon Feb 26 13:29 EST 1996 Received: from gate.texaco.com for SUBRAPS@texaco.com by www.ccl.net (8.7.1/950822.1) id NAA10088; Mon, 26 Feb 1996 13:29:22 -0500 (EST) Received: by gate.texaco.com id AA23598 (Mail SMTP Gateway 3.0 for chemistry@www.ccl.net); Mon, 26 Feb 1996 12:29:13 -0600 Message-Id: Date: 26 Feb 1996 12:19:12 GMT From: "MSBEA01.SUBRAPS" Subject: Summary : Dipole-Dipole Interaction in D To: chemistry@www.ccl.net Comment: MEMO 1996/02/26 12:26 Content-Type: text Content-Length: 4790 Status: R ---------------------------------------------------------------------- THIS MAIL MESSAGE IS FROM THE INTERNET AND MAY HAVE BEEN READ, COPIED, OR MODIFIED BY USERS OTHER THAN INTENDED RECIPIENTS. ---------------------------------------------------------------------- Dear CCL members, A while ago I posted a query on dipole-dipole interactions , the following is a summary of responses that I received. Thanking you all for your time --Mani-- Dr. P. S. Subramanian Fuels and Lubrication Division Texaco Inc. P. O. Box 509 Beacon, NY 12508 email: SUBRAPS@texaco.com vmail: 914-838-7561 Response 1. You have a very strange header above your mail. It sounds almost as if you expect your mail to be tainted by the filth of the transport through internet :-) What does it mean? It was this text that aroused my curiosity, i don't know of any MD packages that do dipole-dipole interaction. Maybe Gromos does it, it seems to be quite advanced. Greetings, Frits Daalmans Frits Daalmans OIO Conformational Analysis Gorlaeus Laboratoria Leiden, The Netherlands E-mail: frits@chemde4.leidenuniv.nl Tel: [+31] (0)71-5274505 Response 2. Dear Dr. P. S. Subramanian Could you summarize responses for your querry on CCL ? Grzegorz Bakalarski ICM Warsaw University Response 3. Hi Mani, To my knowledge only MM3 incorporates such a entity. It uses bond dipoles for such a purpose. Everyone else uses point charges (monopole approximation) to reproduce these properties. If you have a good reason to need the electrostatics (which is probably why you asked the net...) and cannot use a bond dipole scheme, then I would strongly suggest that you perform ab initio calculations, say at the HF/6-31G(d,p) level (or 6-31+G(d,p) if you have anions) and compute the monopole charges from a fit of the electrostatic potential. This method reproduces the molecular dipole moment pretty well; I'm not so sure about the molecular quadrupole moment, though. Use of Mulliken and Natural Bond Order methods is not recommended for this purpose. Be sure that you use a large enough basis set to suitably reproduce the electron density of the systems you are interested in. (As an aside, I stumbled upon this many years ago in grad school by trying to use Mulliken-based charges to reproduce the dipole moments in simple lipids. I failed miserably. In my thinking during that time, I was sure that I could reproduce the molecular dipole from point charges--after all, we all learned it could be done in our fields courses. But of course I was not aware that Mulliken population analysis was not based on trying to reproduce the molecular dipole. It took me a while to realize that it was the method, not the idea, that was at fault.) Hope this helps, Craig -- ----------------------------------+----------------------------------------- Papernet: Craig W. Burkhart | *** GO TRIBE!! *** WORLD SERIES '96 *** Goodyear Research | 142 Goodyear Blvd | 1995 American League Central Div. Champs Akron, OH 44305 | 1995 American League Champion Mouthnet: 216.796.3163 | Faxnet: .3304 | TSN MVP -Albert Belle (50HR,52DB,126RBI) Internet: cburkhart@goodyear.com | TSN Fireman of the Year - Jose Mesa ----------------------------------+----------------------------------------- SPRING TRAINING IS HERE*** SPRING TRAINING IS HERE***SPRING TRAINING IS HERE WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! ---------------------------------------------------------------------------- Response 4. Any package that does molecular dynamics with an MM2-derived force field should include interactions of bond dipoles. (HyperChem does; please contact me for details.) I don't know of any that explicitly include effects of molecular dipoles, but I'm not sure if that's what you were asking about. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ Response 5 Orient 3.2 by Anthony Stone of Cambridge University calculates all sorts of things using electrostatic expansions i.e., charges, dipoles, quadrupoles etc. The new version has basic molecular dynamics in it. If you want a copy you'll have to Email him directly on ajs1@cam.ac.uk and explain who you are and why you want to use it. Darren Andrews. University of Manchester, Department of Chemistry, Oxford road, Manchester. M13 9PL. Darren.Andrews@man.ac.uk PGP: 512/A971A9 Tel: 0161 275 4699. Fax: 0161 275 4598. From sz1296@rzmail.uni-erlangen.de Sat Feb 24 18:44 EST 1996 Received: from max3.rrze.uni-erlangen.de for sz1296@rzmail.uni-erlangen.de by www.ccl.net (8.7.1/950822.1) id SAA24686; Sat, 24 Feb 1996 18:44:46 -0500 (EST) Received: from rzcip01.rrze.uni-erlangen.de by max3.rrze.uni-erlangen.de; Sun, 25 Feb 96 00:44:39 +0100 Received: from local by rzcip01 (SMI-8.6/cl-RRZE) id XAA01318; Sat, 24 Feb 1996 23:44:38 GMT From: Subject: Summary of [W(CO)3(Cp)Cl] To: chemistry@www.ccl.net Date: Sun, 25 Feb 1996 00:44:37 +0100 (MET) Cc: szilagyi@indy.mars.vein.hu X-Mailer: ELM [version 2.4 PL23] Message-Id: <312fa2e755d0002@max3.rrze.uni-erlangen.de> Content-Type: text Content-Length: 1672 Status: RO I posted last year: ************************************************************************* Dear CCL users, A friend of mine who hasn't got a proper access to internet is seeking information about [W(CO)3(Cp)Cl] (Cp= Cyclopentadienyl). (I hope I got that right) He'd like to know something about the use of that substance, spectroscopic data or anything else. As I am NOT subscribed to the CCL, please send a copy of your answer to me, that is: sz1296@rrze.uni-erlangen.de Thank you very much in advance *************************************************************************** These are the responses that I got from CCL-users: 1. firman@dabulls.chem.wisc.edu: (Timothy K. Firman) for info, see: C.Bueno,M.R.Churchill Inorg.Chem., 20, 2197,1981 Which contains a crystal structure. 2. lohrenz@oci.unizh.ch (Dr. John Lohrenz): Try the library! 3. Kieran_Lim@muwayf.unimelb.edu.au: J. Lee, M.G. Humphrey, D.C.R. Hockless, B.W. Skelton, and A.H. White "Mixed Metal Cluster Chemistry. Site-Selective Reactions of CpWIr3(CO)11 with PPh3 and Bidentate Phosphines; X-ray Crystal Structures of CpWIr3(m-dppe)(m-CO)3(CO)6, CpWIr3(m-dppm)(m-CO)3(CO)6 and CpWIr3(m-dppa)(m-CO)3(CO)6." Organometallics, 12 (9), 3468-3473 (1993). Some literature my friend found during his lab: Hoffmann, N.W., Inorganic Chimica Acta, 88 (1984) 59-61 Piper, T.S., Wilkinson G., J. Inorg. Nucl. Chem., 3 (1956) 104 Coffey C. E., Inorg. Nucl. Chem., 3 (1956) 104 here you use W(CO)3(Cp)Cl as an educt. Thank you very much for your valuable hints.