From steinbeck@ice.mpg.de Thu Feb 26 12:10:39 1998 Received: from mjco-s2.ice.mpg.de for steinbeck@ice.mpg.de by www.ccl.net (8.8.3/950822.1) id MAA09612; Thu, 26 Feb 1998 12:01:38 -0500 (EST) Received: from ice.mpg.de (unverified [195.37.47.202]) by mjco-s2.ice.mpg.de (EMWAC SMTPRS 0.83) with SMTP id ; Thu, 26 Feb 1998 18:04:24 +0100 Message-ID: <34F59FED.B969764F@ice.mpg.de> Date: Thu, 26 Feb 1998 18:01:33 +0100 From: Christoph Steinbeck Reply-To: steinbeck@ice.mpg.de To: Computational Chemistry Subject: Java: Subclass of JPanel to display chemical graph Hi, I'd like to announce the availability of a little programming project of mine, called StrucDispPanel. This is a subclass of JPanel (JFC) that takes a connectivity string (no SMILES yet, sorry) and tries to build a rotatable 3D model. This is neither a fully featured 3D model builder nor a modelling tool, but is a conglomerate of SUN's 3D model display and the graph minimizer. It just makes these odd connectivity matrices a little better to view. Also, please note that it's a tool to be used a greater context and not a standalone program. If you are interested in joining me in the development of something more advanced (which also has to be freely available, when it's ready), feel free to contact me. Check http://seneca.ice.mpg.de/~stein/java.html for the program. Cheers, Chris -- Dr. Christoph Steinbeck (mailto:steinbeck@ice.mpg.de - http://seneca.ice.mpg.de/~stein) Max-Planck-Institute of Chemical Ecology (http://www.ice.mpg.de) Tatzendpromenade 1a, 07745 Jena, Germany Tel: int + (49) 3641 643644 --- Fax: int + (49) 3641 643665 There are certain things men must do to remain men. ... Kirk, "The Ultimate Computer," stardate 4929.4.. From youkha@inpharmatics.com Fri Feb 27 14:14:40 1998 Received: from inet1.inetworld.net for youkha@inpharmatics.com by www.ccl.net (8.8.3/950822.1) id NAA03147; Fri, 27 Feb 1998 13:24:12 -0500 (EST) Received: from sydney.inpharma.com (n209060174021.inetworld.net [209.60.174.21]) by inet1.inetworld.net (8.8.7/8.8.7) with SMTP id KAA05444 for ; Fri, 27 Feb 1998 10:24:11 -0800 (PST) Message-ID: <34F70422.6A08@inpharmatics.com> Date: Fri, 27 Feb 1998 10:21:22 -0800 From: Philippe Youkharibache Reply-To: youkha@inpharmatics.com Organization: InPharmatics Corp. To: chemistry@www.ccl.net Subject: [Fwd: Fw: [Circle] The Natural Life Cycle of Mailing Lists] A friend of mine forwarded the following message on "The Natural Life Cycle of Mailing Lists" I thought I might share it with you on the CCL since it has been around for a while, enough to have lived through cycles. Philippe Youkharibache InPharmatics Corp. -----Original Message----- From: Carole To: SeedPods@rattler.cameron.edu Cc: Circle@rattler.cameron.edu Date: Wednesday, February 25, 1998 21:10 PM Subject: [Circle] The Natural Life Cycle of Mailing Lists >The Natural Life Cycle Of Mailing Lists > >Kat Nagel (KatNagel@eznet.net) sent this post to the EARLY-M mailing list in >December 1994. Every list seems to go through the same cycle: > > 1.Initial enthusiasm (people introduce themselves, and gush a lot about how >wonderful it is to find kindred souls). > 2.Evangelism (people moan about how few folks are posting to the list, and >brainstorm recruitment strategies). > 3.Growth (more and more people join, more and more lengthy threads develop, >occasional off-topic threads pop up). > 4.Community (lots of threads, some more relevant than others; lots of >information and advice is exchanged; experts help other experts as well as less >experienced colleagues; friendships develop; people tease each other; newcomers >are welcomed with generosity and patience; everyone -- newbie and expert alike >-- feels comfortable asking questions, suggesting answers, and sharing >opinions). > 5.Discomfort with diversity (the number of messages increases dramatically; >not every thread is fascinating to every reader; people start complaining about >the signal-to-noise ratio; person 1 threatens to quit if *other* people don't >limit discussion to person 1's >pet topic; person 2 agrees with person 1; person 3 tells 1 & 2 to lighten up; >more bandwidth is wasted >complaining about off-topic threads than is used for the threads themselves; >everyone gets annoyed). > 6.Finally: > 1.Smug complacency and stagnation (the purists flame everyone who asks >an 'old' question or responds with humor to a serious post; newbies are >rebuffed; traffic drops to a doze-producing level of a few minor issues; all >interesting discussions happen by private email and are limited to a few >participants; the purists spend lots of time self-righteously congratulating >each other on keeping off-topic threads off the list). > > OR > 2.Maturity (a few people quit in a huff; the rest of the participants >stay near stage 4,with stage 5 popping up briefly every few weeks; many people >wear out >their second or third 'delete' key, but the list lives contentedly ever after). > > > > >============ >Visit The Circle web site at http://rattler.cameron.edu/circle > From ccl@www.ccl.net Fri Feb 27 15:14:42 1998 Received: from ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id PAA03877; Fri, 27 Feb 1998 15:13:57 -0500 (EST) Received: from mmlds1.pha.unc.edu (mmlds1.pha.unc.edu [152.2.147.221]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id PAA12894 for ; Fri, 27 Feb 1998 15:13:55 -0500 (EST) Received: by mmlds1.pha.unc.edu (5.57/TAS/11-16-88) id AA13814; Fri, 27 Feb 98 15:33:04 -0500 Date: Fri, 27 Feb 1998 15:32:59 -0500 (EST) From: Iosif Vaisman To: CCL Subject: Solvation and Complex Formation - International Conference Message-Id: Problems of Solvation and Complex Formation in Solutions 7th International Conference June 29 - July 2, 1998, Ivanovo, Russia Institute of Solution Chemistry of the Russian Academy of Sciences will host the 7th International Conference on Problems of Solvation and Complex Formation in Solutions to be held on June 29 - July 2, 1998 in Ivanovo, Russia. Conference sessions will be organized in three sections: 1. Solvation and reactivity in liquid systems. 2. Role of medium in reactions of complex formation. 3. Chemistry of solutions and new principles of chemical technologies. Previous, 6th Conference was attended by 200 scientists from Russia and FSU, Austria, France, Israel, Poland, Sweden, and UK. Program of the 6th Conference included 70 lectures and 190 posters. It provided a stimulating forum for interaction and discussion between the scientists from various disciplines interested in physics and chemistry of liquids and solutions. Executive Committee A. M. Kutepov, A. G. Zakharov, L. P. Safonova, O. V. Eliseeva Invited Speakers (confirmed) A. K. Baev (Belarus) Karl Heinzinger (Germany) Arkady Kolker (Russia) Boris Krumgalz (Israel) A. K. Lyashchenko (Russia) Yizhak Marcus (Israel) Toshio Yamaguchi (Japan) Call for Abstracts. Abstracts of all conference presentations (plenary and invited lectures, short oral communications, and posters) will be printed in the Book of Abstracts. One-page abstracts should be written in English and submitted in triplicate to Dr. O. V Eliseeva, Institute of Solution Chemistry, Akademicheskaya Street 1, 153045 Ivanovo, Russia or by e-mail to eov@ihnr.polytech.ivanovo.su. Deadline for abstract submission is March 15. Venue. Ivanovo is an industrial and academic center north-east of Moscow. Located within major tourist attraction of Central Russia - The Golden Ring - Ivanovo provides a number of unique opportunities to visit ancient Russian towns, museums, and national parks with breathtaking views on the upper reaches of Volga. Special tours to Vladimir, Suzdal, Kostroma, Ples will be organized for the conference participants. The conference will take place in the Hotel Turist in Ivanovo. Single room - Rbl145 (approx. $25), double room - Rbl130 (including breakfast). Registration fee: general - $150, students - $50 (payable upon arrival at the Conference registration desk). Registration Form Name (first, last) ________________________________________ Title [Prof] [Dr] [Mr] [Mrs] [Ms] Institution _______________________________________________ Address ___________________________________________________ Phone _____________ Fax ____________ E-mail _______________ Title of presentation _____________________________________ Format of presentation [Oral] [Poster] Please submit the registration form before March 15, 1998 to: Conference Secretary Institute of Solution Chemistry Academicheskaya Street 1 153045 Ivanovo, Russia Fax: +7-0932-378509. E-mail: agz@ihnr.polytech.ivanovo.su For additional information visit one of the Conference pages at http://www.ihnr.polytech.ivanovo.su/conference.html or http://sunsite.unc.edu/water/solvation98.html From root@liposome.genebee.msu.su Sun Mar 1 12:15:04 1998 Received: from liposome.genebee.msu.su for root@liposome.genebee.msu.su by www.ccl.net (8.8.3/950822.1) id LAA11294; Sun, 1 Mar 1998 11:16:38 -0500 (EST) Received: from localhost (root@localhost) by liposome.genebee.msu.su (8.8.5/8.8.5) with SMTP id TAA00553 for ; Sun, 1 Mar 1998 19:25:02 +0300 Date: Sun, 1 Mar 1998 19:25:01 +0300 (MSK) From: root To: chemistry Subject: Re: CCL:automatical generation of polypeptide / oligo coordinates? Message-ID: Dear CCLers, few days ago I sent the following request for help: >I'm fairly certain there is a program/script capable of generating a >polypeptide / oligo e.g. in linear conformation just from the primary >structure (amino acid sequence) data somewhere out there. Corina-generated >structures from SMILES seem to lack important data, preventing both XPLOR >and Solvate from reading them (? -- feel free to correct me). I wanted to >generate pdb/psf pairs 10-30 residue-oligos for subsequent MD runs. So far, I've received the followinig pointer by Paul Beroza (thanks Paul!): > Hi Eugene, > > I wrote a program do construct polypeptide structures from the > primary sequence and a file specifying the type of structure > desired (extended, alpha helical, etc.). It is written in "nab", > a language that was developed to model large biomolecules. You > can find more information on David Case's web page: > http://www.scripps.edu/case > > Paul Beroza > CombiChem Inc. I have not tried his package yet, as I have discovered that protein, a part of the Tinker suite http://dasher.wustl.edu/tinker/ can do what I wanted (it compiles with f77 under Linux; the following polylysine 50-mer has been made with the protein tool: http://liposome.genebee.msu.su/gifs/polylys-50-mer-chlorides.gif (structure not minimized yet, chloride counterions added manually). Btw, the problems with Solvate unable to handle Corina-generated structures had to do with the redid-id (fourth column in the pdb file) being zero. By setting it manually to one I have finally managed to hydrate my nonprotein polyelectrolytes with Solvate. Apropos Solvate: there seems to be an atof bug in a Linux library (?) which makes the program scan garbage from the -t (thickness) command line argument. Had somebody experienced similiar difficulties? (To fix it, I think I'll either upgrade the libraries, or make a (kludgey) workaround with (double) atoi). Regards, Eugene Leitl From David.DeVito@chiphy.unige.ch Mon Mar 2 06:15:21 1998 Received: from sc2a.unige.ch for David.DeVito@chiphy.unige.ch by www.ccl.net (8.8.3/950822.1) id FAA16259; Mon, 2 Mar 1998 05:49:45 -0500 (EST) Received: from PCC2340E.unige.ch ([129.194.52.14]) by sc2a.unige.ch (PMDF V5.1-10 #10385) with SMTP id <01IU6UFLE4UG003IOM@sc2a.unige.ch> for chemistry@www.ccl.net; Mon, 2 Mar 1998 11:49:44 MET Date: Mon, 02 Mar 1998 11:49:52 +0100 From: David De Vito Subject: Problem with Internal Coordinates with GAMESS To: CCL Message-id: <001a01bd45c8$eecc8b00$0e34c281@PCC2340E.unige.ch> MIME-version: 1.0 X-Mailer: Microsoft Outlook Express 4.72.2106.4 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7bit X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 X-Priority: 3 Dear CCLers, I am a beginner with the program GAMESS and I am trying to do an optimization with internal coordinates. Something is wrong with my internal coordinates choice, but I don't understand where the problem is... I get the following error message: ROUNDOFF ERROR IN BEND - STOP This is my geometry input $DATA Rh(H2O)6 sym Th GS RHF/SBK OPT TH 0 RH1 45.0 0.0000000000 0.0000000000 0.0000000000 SBK 0 O2 8.0 0.0000000000 0.0000000000 2.0660352799 N31 6 D 1 1 1.2000000000 1.00000000 H3 1.0 0.7799470589 0.0000000000 2.6209486352 N31 6 $END $ZMAT IZMAT(1)= 1, 1, 2, 1, 1, 3, 1, 1, 4, 1, 1, 5, 1, 1, 6, 1, 1, 7, 2, 3, 1, 5, 2, 6, 1, 3, 2, 6, 1, 5, 2, 7, 1, 3, 2, 7, 1, 5, 2, 2, 1, 5, 2, 2, 1, 6, 2, 4, 1, 3, 2, 4, 1, 6, 1, 2, 8, 1, 2, 10, 2, 8, 2, 1, 2, 10, 2, 1, 3, 8, 2, 1, 5, 3, 10, 2, 1, 5, 1, 3, 9, 1, 3, 11, 2, 9, 3, 1, 2, 11, 3, 1, 3, 9, 3, 1, 5, 3, 11, 3, 1, 5, 1, 4, 12, 1, 4, 13, 2, 12, 4, 1, 2, 13, 4, 1, 3, 12, 4, 1, 3, 3, 13, 4, 1, 3, 1, 5, 14, 1, 5, 15, 2, 14, 5, 1, 2, 15, 5, 1, 3, 14, 5, 1, 3, 3, 15, 5, 1, 3, 1, 6, 17, 1, 6, 18, 2, 17, 6, 1, 2, 18, 6, 1, 3, 17, 6, 1, 3, 3, 18, 6, 1, 3, 1, 7, 16, 1, 7, 19, 2, 16, 7, 1, 2, 19, 7, 1, 3, 16, 7, 1, 3, 3, 19, 7, 1, 3, $END ---------------------------- Can somebody help me with this input ? I would appreciate any suggestions. Thanks in advance. D. De Vito. **************************************************************** D. De Vito Department of Physical Chemistry Group of Prof. Weber (Computational Chemistry) University of Geneva Office 106 - Sciences II 30, Quai Ernest-Ansermet 1211 Geneva 4 / Switzerland +4122 / 702.65.35 (Office) +4179 / 310.05.76 (Mobile) +4122 / 733.38.35 (Home) http://lcta/~devito (Personal Page) http://www.unige.ch/sciences/chimie (Web Master) **************************************************************** From dobado@cica.es Mon Mar 2 08:15:16 1998 Received: from mailgw.cica.es for dobado@cica.es by www.ccl.net (8.8.3/950822.1) id HAA16612; Mon, 2 Mar 1998 07:31:04 -0500 (EST) Received: from dismol9.ugr.es (dismol9.ugr.es [150.214.18.189]) by mailgw.cica.es (8.8.8/8.8.8) with ESMTP id NAA22246 for ; Mon, 2 Mar 1998 13:29:30 GMT Message-ID: <34FA9727.535A7FD3@cica.es> Date: Mon, 02 Mar 1998 13:25:29 +0200 From: "Jose A. Dobado" Reply-To: dobado@cica.es Organization: Universidad de Granada X-Mailer: Mozilla 4.01 [en] (Win95; I) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: CCL: Re: Urea dimer/oligomers ab initio/semiempirical ? X-Priority: 3 (Normal) Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Shridhar, see our paper and references therein: J.A. Dobado, J. Molina and D. Portal Olea "A Theoretical Study on the Urea-Hydrogen Peroxide 1:1 Complexes. " Journal of Physical Chemistry A, 102, 778 (1998) maybe it can help you. Cheers, Jose gadre@cdac.ernet.in wrote: > Dear Sirs and Madams : > Are you aware of any ab initio/semi-empirical RECENT study on > urea dimer, trimer and higher aggregate formation? > We are interested in understanding the how and why of this process. > Any information on energetics, geometries etc. will be welcome. > Thanking you in advance...............Shridhar Gadre > > --- > Administrivia: This message is automatically appended by the mail > exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: > Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: > www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive > search > Web: http://www.ccl.net/chemistry.html > --- -- _/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/ Universidad de Granada | Jose A. Dobado, PhD. Facultad de Ciencias | Dpto. Quimica Organica | Tel/Fax: +34-(9)58-243186 Avda. Fuentenueva /sn | http://www.ugr.es/~dobado E-18071 Granada (Espaņa) | dobado@cica.es _/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/-_/ From ramon@ce.ifisicam.unam.mx Mon Mar 2 16:15:21 1998 Received: from ce.ifisicam.unam.mx for ramon@ce.ifisicam.unam.mx by www.ccl.net (8.8.3/950822.1) id PAA25257; Mon, 2 Mar 1998 15:33:51 -0500 (EST) Message-Id: <199803022033.PAA25257@www.ccl.net> Received: by ce.ifisicam.unam.mx (1.38.193.4/16.2) id AA13349; Mon, 2 Mar 1998 14:28:52 -0600 From: Ramon Garduno Subject: Printer administrator?? To: CHEMISTRY@www.ccl.net (CCL POST MSG) Date: Mon, 2 Mar 98 14:28:51 CST Mailer: Elm [revision: 70.85] Dear CCLers; With Jan Labanowsky permition I would like to ask all of you, if there is such a thing as a "Printer Administrator" for UNIX systems. This is what I need: A demon or something like that, that can assign to each user a printing permit, so that students can be controlled or denied printing privileges. Much obliged, -- "..... un pais se concidera mas civilizado cuando sus leyes tienen la sabiduria y la eficiencia para evitar que un hombre debil se vuelva mas debil y que un hombre poderoso se vuelva demasiado poderoso." Si Este Es un Hombre - Primo Levi ____________________________________________________________________________ Dr. Ramon Garduno-Juarez Research Professor in Biophysics INSTITUTO DE FISICA | EMAIL: ramon@ce.ifisicam.unam.mx UNIVERSIDAD NAL. AUTONOMA DE MEXICO | rgard@redvax1.dgsca.unam.mx Laboratorio de Cuernavaca | VOICE: (5)6227749 ; (73)291749 Apdo. Postal 48-3 | (73)111611 & (73)175388 62251 Cuernavaca, Morelos | FAX: (5)6227775 & (73)291775 MEXICO | (73)173077 ___________________________________ EOF _____________________________________ From ponder@dasher.wustl.edu Mon Mar 2 16:24:41 1998 Received: from dasher.wustl.edu for ponder@dasher.wustl.edu by www.ccl.net (8.8.3/950822.1) id PAA25346; Mon, 2 Mar 1998 15:45:01 -0500 (EST) From: Received: from localhost by dasher.wustl.edu (5.65v3.2/1.1.10.5/12Feb97-1108AM) id AA17402; Mon, 2 Mar 1998 14:44:59 -0600 Message-Id: <9803022044.AA17402@dasher.wustl.edu> Reply-To: ponder@dasher.wustl.edu To: chemistry@www.ccl.net Cc: ponder@dasher.wustl.edu Subject: TINKER Version 3.6 is Available Date: Mon, 02 Mar 98 14:44:59 -0600 X-Mts: smtp Dear CCL, The latest release of the TINKER molecular modeling package, version 3.6 dated February 1998, is available from http://dasher.wustl.edu/tinker/ or via anonymous ftp from dasher.wustl.edu in the /pub/tinker area. TINKER is a modular, general package for molecular mechanics and dynamics with some special facilities and parameter sets for peptides and proteins. It supports AMBER-95, CHARMM, MM2, MM3, AMBER/OPLS and OPLS-AA. Some very preliminary parameters for our TINKER polarizable multipole force field are also included. The package contains advanced algorithms for energy minimization, distance geometry and global search that are not, to our knowledge, available elsewhere. TINKER is distributed with full source code, a User's Guide, and several examples and test molecule files. Directions are supplied for building the package on many Unix variants, Windows 95/NT and Macintosh. Prebuilt executables limited to a maximum of 3000 atoms are also provided for Windows 95/NT and Power Macintosh. Please see the web site above for further information. Comments, questions and suggestions for future improvements (yes, we are looking into a GUI...) can be sent to ponder@dasher.wustl.edu. Jay Ponder -------- Jay W. Ponder Phone: (314) 362-4195 Biochemistry, Box 8231 Fax: (314) 362-7183 Washington University Medical School 660 South Euclid Avenue Email: ponder@dasher.wustl.edu St. Louis, Missouri 63110 USA WWW: http://dasher.wustl.edu/