From ccl@www.ccl.net Tue Feb 25 06:25:27 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id FAA22069; Tue, 25 Feb 1997 05:58:39 -0500 (EST) Received: from mail-d.bcc.ac.uk for leslie@ri.ac.uk by bedrock.ccl.net (8.8.3/950822.1) id FAA28462; Tue, 25 Feb 1997 05:58:37 -0500 (EST) Received: from ri.ac.uk (actually davy.ri.ac.uk) by mail-d.bcc.ac.uk with SMTP (PP); Tue, 25 Feb 1997 10:58:00 +0000 Received: from faraday.ri.ac.uk by ri.ac.uk (5.x/SMI-SVR4) id AA14319; Tue, 25 Feb 1997 11:00:49 GMT Received: from localhost by faraday.ri.ac.uk (950413.SGI.8.6.12) id LAA03382; Tue, 25 Feb 1997 11:00:49 GMT Date: Tue, 25 Feb 1997 11:00:49 +0000 (WET) From: "Prof. Leslie Glasser" X-Sender: leslie@faraday To: chemistry@ccl.net Subject: CCL: crystal packing calculations Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Further potentially useful references to crystal packing attempts: 'Ab initio Prediction of Polymorphs', FJJ Leusen, J Cryst. Growth (1996) 166(1-4), 900-3 - a brief review and some recent applications. 'Predicting the Crystal Structure of Organic Molecular Materials', AM Chaka, et al., Acta Cryst. (1996) B52(1), 165-183 - describes a new program for rigid molecules, which selectively searches only the most likely 13 space groups (a la Kitaigorodskii). 'Calculations on Crystal Packing of a Flexible Molecule: Leu-Enkephalin' L Glasser and HA Scheraga, J Mol Biol. (1988) 199, 513-524 - an early trial-and-error attempt (a la Kitaigorodskii) at packing a flexible molecule, and the consequences of H-bonding. Leslie (Prof) L. Glasser glasser@aurum.chem.wits.ac.za [Dept. Chemistry, Univ. Witwatersrand, Johannesburg, S. Africa] Mailing address until July, 1997: Chemical Crystallography, Inorganic Chemistry Lab., 9 Parks Road, Oxford OX1 3QS, England Tel: Intl + 44 1865 270 832 FAX: Intl + 44 1865 272 699 Institutional address: Royal Institution of Great Britain Tel: Intl + 44 + 171-409-2992 21 Albemarle St., FAX: Intl + 44 + 171-629-3569 London W1X 4BS, UK E-mail: leslie@ri.ac.uk From ccl@www.ccl.net Tue Feb 25 10:28:38 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id KAA23821; Tue, 25 Feb 1997 10:17:19 -0500 (EST) Received: from gibbs.oit.unc.edu for tropsha@gibbs.oit.unc.edu by bedrock.ccl.net (8.8.3/950822.1) id KAA04084; Tue, 25 Feb 1997 10:17:19 -0500 (EST) Received: by gibbs.oit.unc.edu (8.7.5/10.1) id KAA07346; Tue, 25 Feb 1997 10:17:19 -0500 (GMT+5:00) Date: Tue, 25 Feb 1997 10:17:16 -0500 From: Alex Tropsha To: CCL Subject: CCL: Mol2 to SMILES Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi folks: Can anyone provide me with a link to a free software that converts mol and/or mol2 files to SMILES. Thanks a lot. =Alex Tropsha= xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx x Alexander Tropsha, Ph.D. x x Assistant Professor, Director x x the Laboratory for Molecular Modeling x x CB # 7360, Beard Hall x x School of Pharmacy x x University of North Carolina x x Chapel Hill, NC 27599-7360 x x Tel. (919) 966-2955 x x Fax (919) 966-6919 x xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx From ccl@www.ccl.net Tue Feb 25 10:30:59 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id KAA23760; Tue, 25 Feb 1997 10:09:50 -0500 (EST) Received: from gig.usda.gov for srheller@gig.usda.gov by bedrock.ccl.net (8.8.3/950822.1) id KAA03676; Tue, 25 Feb 1997 10:09:49 -0500 (EST) Received: by gig.usda.gov (5.x/SMI-SVR4) id AA26363; Tue, 25 Feb 1997 10:06:39 -0500 Date: Tue, 25 Feb 1997 10:06:38 -0500 (EST) From: "Stephen R. Heller" To: jcicshelp , chemistry@ccl.net, chminf-l@iubvm.ucs.indiana.edu, orgchem@extreme.chem.rpi.edu Subject: Additional chemistry software for review Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Subject: More Software and Database for Review February 25, 1997 Subject: Computer Software for Review As the Software Review Editor for the ACS Journal of Chemical Information and Computer Science (JCICS) I often get software for review in the journal. Today I have 2 additional new software products. I am looking for people who are willing to review these software products. In return for the review which is published in JCICS you get to keep the software or database. The review should be completed in 1-3 months. The length of the review is 4-10 double spaced typed pages. Sample reviews can be found in most of the recent issues of JCICS. Please try to give me some (short) reason to choose you over another person. DO NOT SAY YOU WILL REVIEW ANYTHING I HAVE AVAILABLE. Messages with such replies are trashed! I have tried this approach for about the past five years and it is working reasonably well. (REMINDER: For those who haven't finished your reviews of software sent months and months ago, this last sentence does not apply to you!) As a result, I am continuing this new method to find reviewers using this e- mail/user group system. I reserve the right to abandon this if it is a problem, or inappropriate. I will not notify people if I have found a reviewer. If you don't hear from me within a few days I have chosen someone else to review the particular package. As I get many, many, (too many) replies to this message, please do not respond after 28 February 1997 (Friday), as I am sure the software will be gone by then. I can be reached on Internet (SRHELLER@GIG.USDA.GOV). PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE, and FAX NUMBER!!! (I send the software by Federal Express.) Without this information I WILL NOT consider your request. Steve Heller The packages I now have are: 1. MoleCalc A new chemistry shareware software product for Apple Macintosh computers titled MoleCalc. The program is a must for practicing chemists and students alike. Chemistry teachers will appreciate the ability to demonstrate the importance of significant figures and uncertainty in atomic weights. Features: * Enter and display formulas using standard chemical notation with the ease of the Apple Macintosh graphical user interface * Select constituent elements of compounds quickly using the standard "Periodic Table" layout via mouse clicks without the need for keyboard input * Calculate atomic weight of compounds containing any of the known 109 elements * Calculate atomic weight of compounds containing commonly used stable isotopes * Calculated atomic weight can be displayed to the correct significant digits depending upon the selected constituent elements * Calculates uncertainty in the calculated atomic weight based upon the entered elements constituent in the compound * Calculates weights and uncertainties based on the 1989 Report of the Commission on Atomic Weights and Isotopic Abundances of the IUPAC * Displays Hill formula for entered compound * Displays weight percent or weight fraction of each constituent element of the entered compound * Supports cut & paste for transfer of calculated results to other applications such as spreadsheets or wordprocessors 2.Periodic A chemistry shareware software product for Apple Macintosh computers titled Periodic. This periodic table database has numerous unique features and contains 27 data fields of information for each of the currently known 112 elements. All data can be viewed graphically by period, group or for all known elements. Features: * Select data for desired element(s) quickly using the standard "periodic table" layout without keyboard input. * Display information from 27 different data fields for each of the known 112 elements. * Slider control allows highlighting of elements displaying desired property or satisfying choosen condition(s). * Graphing of all numeric elemental properties by period, group or for all known elements. * Label groups using the European, USA or IUPAC standard. * Supports Cut & Paste for transfer of results to other applications such as spreadsheet or wordprocessor. * Full on-line help Both programns are from: Digital Chemistry Company, PO Box 332M, Manunda, Cairns 4870 Australia. Fax: +61 70 322 756 Email: digichem@internetnorth.com.au From kanzaki@mxk.meshnet.or.jp Tue Feb 25 20:25:42 1997 Received: from meshsv81.tk.mesh.ad.jp for kanzaki@mxk.meshnet.or.jp by www.ccl.net (8.8.3/950822.1) id TAA28316; Tue, 25 Feb 1997 19:37:19 -0500 (EST) Received: from tw3181 (tkrz1DS11.stm.mesh.ad.jp [133.205.230.161]) by meshsv81.tk.mesh.ad.jp (8.8.4+2.7Wbeta4/3.5Wpl1-) with SMTP id JAA01684 for ; Wed, 26 Feb 1997 09:37:13 +0900 (JST) Message-Id: <199702260037.JAA01684@meshsv81.tk.mesh.ad.jp> X-Sender: kanzaki@mxk.meshnet.or.jp (Unverified) X-Mailer: Windows Eudora Pro Version 2.2-Jr1 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-2022-JP" Date: Wed, 26 Feb 1997 09:40:31 +0900 To: ccl From: =?ISO-2022-JP?B?IhskQj9AOmohITkvPCMbKEoiIA==?= Subject: radical on aromatic ring Dear All, I am trying to estomate the tendencey to radical formation and stability of radical cation on aromatic ring (benzene or indole). Does anyone know how to caluculate? I should use semiempirical or ab initio method? I will summarize. Thank you in advance. Koji Kanzaki -------------------------------------------------------- KANZAKI KOJI( Yoshitomi Pharmaceutical Industries, LTD ) 7-25 Koyata 3-chome, Iruma-shi, Saitama, 358, JAPAN e-mail: kanzaki@mxk.meshnet.or.jp Fax: +81-429-63-3121 Phone: +81-429-64-1906 >From microsim@nis.net Mon Feb 24 23:24 EST 1997 Received: from maple.nis.net for microsim@nis.net by www.ccl.net (8.8.3/950822.1) id XAA19249; Mon, 24 Feb 1997 23:24:54 -0500 (EST) Received: from PACKARDBELL1 by maple.nis.net with smtp (Smail3.1.28.1 #2) id m0vzFJE-0010p2C; Tue, 25 Feb 97 00:20 EST Message-ID: <33129364.9D8@nis.net> Date: Mon, 24 Feb 1997 23:23:16 -0800 From: Willie Cui Organization: microsimulations MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: AccuModel v1.1 with ISIS/Draw Add-in, available to download for evaluation Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 [Edited by CCL administrator] We have place the fully functional demo of AccuModel 1.1 for Windows 95 & NT up on our WWW site. AccuModel is the most intuitive and accurate program for the construction of 3D molecular structures, using the MM3 force field, and operating on PC and PowerMac. This new version is a significant upgrade with many added features and improvements. Among them, AccuModel as ISIS/Draw and ISIS/base Add-in that completely eliminate the barrier between 2D and 3D chemical information. You can download this fully functional program for 30 days free evaluation. http://www.microsimulations.com/download.html The user guide in the format of Microsoft Word can also be downloaded from the same page. For more information visit the URL: ftp://www.ccl.net/pub/chemistry/info/software-packages/accumodel.note Enjoy! -- Willie Cui voice: 201-512-0486 MicroSimulations fax: 201-512-0489 478 Green Mountain Road email: info@microsimulations.com Mahwah, NJ 07430 URL: http://www.microsimulations.com From shin@hermes.fju.edu.tw Wed Feb 26 02:25:41 1997 Received: from hermes.fju.edu.tw for shin@hermes.fju.edu.tw by www.ccl.net (8.8.3/950822.1) id BAA00318; Wed, 26 Feb 1997 01:31:57 -0500 (EST) Received: by hermes.fju.edu.tw (AIX 3.2/UCB 5.64/4.03) id AA08141; Wed, 26 Feb 1997 14:05:36 +0800 Date: Wed, 26 Feb 1997 14:05:36 +0800 From: shin@hermes.fju.edu.tw (Shin-Inn Chen) Message-Id: <9702260605.AA08141@hermes.fju.edu.tw> To: chemistry@www.ccl.net Subject: visualization program dear netter: there are lots of information about visualization program recently. dose anyone know which of them support effective core potential (ECPS) calculation? we would like to find a program for visualizing the results obtained from gaussian94. we have considered MOLDEN, but it dose not support the ECPS calculation. thanks for your help :) shin 97/2/26 e-mail: shin@hermes.fju.edu.tw From dsmith@CTCnet.Net Wed Feb 26 09:25:43 1997 Received: from home.CTCnet.Net for dsmith@CTCnet.Net by www.ccl.net (8.8.3/950822.1) id IAA02616; Wed, 26 Feb 1997 08:41:56 -0500 (EST) Received: from fock by home.CTCnet.Net (SMI-8.6/SMI-SVR4) id IAA07590; Wed, 26 Feb 1997 08:37:41 -0500 Date: Wed, 26 Feb 1997 08:37:41 -0500 Message-Id: <199702261337.IAA07590@home.CTCnet.Net> X-Sender: dsmith@pop.dasgroup.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Priority: 1 (Highest) To: CHEMISTRY@www.ccl.net From: dsmith@CTCnet.Net (Douglas A. Smith Ph.D.) Subject: 2nd notice: Survey According to the report, Technology Vision 2020: The U.S. Chemical Industry, released last month by the American Chemical Society, the first two key steps in meeting challenges during the next 25 years requires = generation and use of new knowledge, and = capitalizing on information technology. Computational technologies were considered a key enabling technology area to achieve these goals. In particular, Technology Vision 2020 suggested that industry should "support further development of high-performance desktop workstations, large and fast vector-processor machines, and highly parallel processors." We agree, and would like to get the input of the computational chemistry, molecular modeling and simulation, and structural chemistry community. In order to get the views of the CCL community, I am requesting your participation in our survey, which The DASGroup, Inc. (DASGroup) is using to gain an understanding of current hardware and software utilization and future trends within the chemical industry. Feel free to tell a colleague about this survey as well. While a limited number of surveys were sent via U. S. mail to U. S. companies, I would appreciate it if you would take the time to fill in the survey on our web page at = www.dasgroup.com As an incentive, any company employee completing a survey will be entered into a drawing to win a Compaq PaC companion handheld computer with 4 Mb of RAM and running Windows CE. (Sorry, the drawing is not open to academics, students, or government employees.) We appreciate you taking the time to respond to our survey. Doug Smith -- Dr. Douglas A. Smith, President and CEO | voice: (814) 255-7859 The DASGroup, Inc. | fax: (814) 255-3517 1732 Lyter Drive, 2nd Floor | email: dsmith@dasgroup.com Johnstown, PA 15905 | WWW: http://www.dasgroup.com Contract R&D specialists in modeling, simulation, synthesis and risk assessment for chemistry, materials science, and biotechnology. From Alan.Shusterman@directory.Reed.EDU Wed Feb 26 14:25:45 1997 Received: from reed.edu for Alan.Shusterman@directory.Reed.EDU by www.ccl.net (8.8.3/950822.1) id OAA05174; Wed, 26 Feb 1997 14:19:25 -0500 (EST) Received: from isis.Reed.EDU [134.10.2.1 no identification] by reed.edu (/\oo/\ Smail3.1.29.1osf1 #29.2) id ; Wed, 26 Feb 97 11:19 PST Message-id: <2660127@isis.Reed.EDU> Date: 26 Feb 97 11:19:32 PST From: Alan.Shusterman@directory.Reed.EDU (Alan Shusterman) Subject: methane dimer To: CHEMISTRY@www.ccl.net Can anyone tell me the experimental CC distance in methane dimer, and the binding energy of the dimer relative to the individual molecules? Literature refs, if you can easily lay your hands on them, are also much appreciated. Thanks, Alan Shusterman Department of Chemistry Reed College Portland, OR alan@reed.edu From 100622.3264@CompuServe.COM Wed Feb 26 14:36:31 1997 Received: from dub-img-2.compuserve.com for 100622.3264@CompuServe.COM by www.ccl.net (8.8.3/950822.1) id OAA05079; Wed, 26 Feb 1997 14:01:30 -0500 (EST) Received: by dub-img-2.compuserve.com (8.6.10/5.950515) id OAA17322; Wed, 26 Feb 1997 14:01:01 -0500 Date: 26 Feb 97 12:36:41 EST From: Henry Stewart Pubs <100622.3264@CompuServe.COM> To: Computational Chemistry Subject: Bioinformatics Conference Message-ID: <970226173641_100622.3264_BHL67-1@CompuServe.COM> Henry Stewart Conference Studies is holding a One-Day Conference on"Successfully Integrating Bioinformatics into Drug Discovery" on Wednesday, 30 April 1997 at The Cafe Royal, London W1. Speakers include Dr Mark Cortelyou from Oxford Molecular Group, Dr Tom Flores and Dr Chris Sander from EMBL - EBI, Dr Stuart Green from the University of Leeds, UK, Dr Diana Hill from Xenova Ltd, Professor Rod Hubbard from the University of York, UK, Dr Andrew Lyall from Glaxo Wellcome R & D, and Dr Tony Parsons from Pfizer Central Research. The fee for the conference is L365/$625 plus VAT at 17.5%. There is a special rate for academics at L250 plus VAT. For further enquiries or details on the programme conference, please contact Kavita Nayar, Henry Stewart Conference Studies, Russell House, 28/30 Little Russell Street, London WC1A 2HN, tel: +44 (0) 171-404 3040, fax: +44 (0) 171-404 2081, email: 100622.3264@compuserve.com From Y0H8797@ACS.TAMU.EDU Wed Feb 26 15:25:56 1997 Received: from VMS1.TAMU.EDU for Y0H8797@ACS.TAMU.EDU by www.ccl.net (8.8.3/950822.1) id PAA05895; Wed, 26 Feb 1997 15:20:00 -0500 (EST) Date: Wed, 26 Feb 1997 14:20:02 -0600 (CST) From: YONG HUANG To: CHEMISTRY@www.ccl.net Message-Id: <970226142002.2085f4eb@ACS.TAMU.EDU> Subject: Problem to ftp CAChe ouput file on Mac I set up my Mac as a ftp server. After the calculation is done, a file folder named MyMolf is generated for molecule file MyMol. The problem is when you access the ftp server from a remote site, MyMolf can't be entered ("Directory not found") or MyMolf is simply shown as MyMold or MyMol plus a special character or something else. There's no way to get into this folder although I tried most letters. What's wrong? I'm using NCSA Telnet on the Mac. I ftp to it through VMS and UNIX. Thank you for your help. Yong [Note: A few people pointed out to me to the effect that electronic delocalization is artifact. Let me read some literature and think a while before I respond. Thank you, gentlemen.]