From owner-chemistry@ccl.net Wed Oct 11 00:09:36 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id XAA12343; Tue, 10 Oct 1995 23:59:58 -0400 Received: from rani.chem.yale.edu for lim@rani.chem.yale.edu by bedrock.ccl.net (8.6.10/950822.1) id XAA09514; Tue, 10 Oct 1995 23:59:47 -0400 Received: by rani.chem.yale.edu; Tue, 10 Oct 95 23:59:24 -0400 From: Dongchul Lim Message-Id: <9510110359.AA01412@rani.chem.yale.edu> Subject: public domain 3D structure to SMILES translator To: chemistry@ccl.net (Computational Chemistry) Date: Tue, 10 Oct 95 23:59:23 EDT X-Mailer: ELM [version 2.3 PL11] Are there any public domain or free 3D molecular structure to SMILES translators? -D. Lim, lim@rani.chem.yale.edu From owner-chemistry@ccl.net Wed Oct 11 04:24:44 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id EAA23062; Wed, 11 Oct 1995 04:12:12 -0400 Received: from techunix.technion.ac.il for chr07pa@techunix.technion.ac.il by bedrock.ccl.net (8.6.10/950822.1) id EAA10879; Wed, 11 Oct 1995 04:12:08 -0400 Received: (from chr07pa@localhost) by techunix.technion.ac.il (8.6.12+/8.6.10) id KAA16861; Wed, 11 Oct 1995 10:12:02 +0200 Date: Wed, 11 Oct 1995 10:12:02 +0200 (EET) From: Pauncz Ruben To: LIST CC cc: c@techunix.technion.ac.il Subject: subscription to chemistry Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I would like to subscribe to the chemistry list distributed by chemistry@www.ccl.net. Thank you for putting my announcement on your list. Best regards Ruben Pauncz *-------------------------------------------* | Dr. Ruben Pauncz, Professor Emeritus | | Department of Chemistry | | Technion - Israel Institute of Technology | | Haifa 32000, Israel | | | | CHR07PA@TECHNION.TECHNION.AC.IL | | Telephone: +972-4-293743 | | Fax: +972-4-233735 | *-------------------------------------------* From owner-chemistry@ccl.net Wed Oct 11 04:54:46 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id EAA23571; Wed, 11 Oct 1995 04:43:52 -0400 Received: from dub-img-2.compuserve.com for 100317.2656@compuserve.com by bedrock.ccl.net (8.6.10/950822.1) id EAA10957; Wed, 11 Oct 1995 04:43:50 -0400 Received: by dub-img-2.compuserve.com (8.6.10/5.950515) id EAA26212; Wed, 11 Oct 1995 04:43:21 -0400 Date: 11 Oct 95 04:41:22 EDT From: Herbert Koeppen <100317.2656@compuserve.com> To: "Comput. Chem. List CCL" Subject: Book/review articles on forcefields Message-ID: <951011084122_100317.2656_GHW94-2@CompuServe.COM> On October 10, 1995, Tosh wrote: > Does anyone out there know of a good book or review article on forcefields? > In particular, my colleagues are interested in any articles which may aid > in choosing the 'best' forcefield for a particular problem - if such a > thing exists (I know it is rather subjective, but they would appreciate any > leads). Tosh, have a look at Burkert & Allinger "Molecular Mechanics", ACS Monograph 177, 1982. More recent information can be found in Lipkowitz & Boyd "Reviews in Computational Chemistry", VCH, Vol. 2 (1991) and Vol. 6 (1995). Herbert -------------------------------------------------------------------------------- Herbert Koeppen, PhD, Medicinal Chemistry Department, Boehringer Ingelheim KG, D-55216 Ingelheim, Germany phone: ++49-6132-776845, fax: ++49-6132-773418 e-mail: 100317.2656@compuserve.com From owner-chemistry@ccl.net Wed Oct 11 07:54:44 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id HAA25695; Wed, 11 Oct 1995 07:48:56 -0400 Received: from sangam.ncst.ernet.in for ipcakc@ipc.iisc.ernet.in by bedrock.ccl.net (8.6.10/950822.1) id HAA11490; Wed, 11 Oct 1995 07:48:35 -0400 Received: from postoffice.iisc.ernet.in (twisha.ece.iisc.ernet.in [144.16.64.4]) by sangam.ncst.ernet.in (8.6.12/8.6.6) with ESMTP id RAA09063 for ; Wed, 11 Oct 1995 17:19:18 +0530 Received: by postoffice.iisc.ernet.in (ERNET-IISc/SMI-4.1) id FAA00093; Wed, 11 Dec 1985 05:08:03 +0500 Date: Wed, 11 Dec 1985 05:08:03 +0500 From: ipcakc@ipc.iisc.ernet.in (Dr.A.K.Chandra) Message-Id: <198512110008.FAA00093@postoffice.iisc.ernet.in> To: CHEMISTRY@ccl.net Subject: change of address Dear Jan, Please not that my address (e-mail) has been changed to ipcakc@postoffice.iisc.ernet.in from ipcakc@vigyan.iisc.ernet.in and I request your goodself to kindly pass my all CCL messages to the new address. Thank you in advance and inconvenience is sincerely regretted. Sincerely, A.K. Chandra From dimitris@3dp.com Wed Oct 11 08:24:44 1995 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.6.10/950822.1) id IAA26063; Wed, 11 Oct 1995 08:11:48 -0400 Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA20498; Wed, 11 Oct 95 08:14:45 -0400 Received: by europa.3dp.com (931110.SGI) id AA29747; Wed, 11 Oct 95 08:13:07 -0400 From: "Dimitris Agrafiotis" Message-Id: <9510110813.ZM29745@europa.3dp.com> Date: Wed, 11 Oct 1995 08:13:07 -0400 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@www.ccl.net Subject: [Sum] Pauling formula for vdw radii Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Pauling's 'formula' for estimating vdw radii based on atomic radii is indeed very simple: Rvdw = Ra + 0.8 (source "The Nature of the Chemical Bond" by L. Pauling). Thanks to those who responded. Ciao, -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com Principal Research Scientist | tel: (610) 458-6045 3-Dimensional Pharmaceuticals, Inc. | fax: (610) 458-8249 665 Stockton Drive, Suite 104 Exton, PA 19341 From owner-chemistry@ccl.net Wed Oct 11 09:24:45 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id JAA27839; Wed, 11 Oct 1995 09:19:01 -0400 Received: from duke.cs.duke.edu for taisung@chem.duke.edu by bedrock.ccl.net (8.6.10/950822.1) id JAA12261; Wed, 11 Oct 1995 09:18:59 -0400 Received: from london.chem.duke.edu by duke.cs.duke.edu (5.65/3.10G/4.1.3) id AA02060; Wed, 11 Oct 95 09:18:59 -0400 Received: from debye.chem.duke.edu by london.chem.duke.edu (5.64/1.19LP/4.1.1) id AA14693; Wed, 11 Oct 95 09:18:57 -0400 Received: by debye.chem.duke.edu (8.6.8.1/2.12L/4.1) id JAA17964; Wed, 11 Oct 1995 09:18:56 -0400 Date: Wed, 11 Oct 1995 09:18:55 -0400 (EDT) From: Taisung Lee To: chemistry@ccl.net Subject: PC as a file server? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Our group is looking for a machine as a file server via NFS. We are considering to buy a high end PC running Linux or WindowsNT. Is there anybody has experiences about that? We will connect the file server to 3 IBM RS/6000s and one SGI/R4000. Is there any problem of compatibilty? Thanks in advance for any reply. Taisung Lee (taisung@chem.duke.edu) From netsci@awod.com Wed Oct 11 09:39:45 1995 Received: from sumter.awod.com for netsci@awod.com by www.ccl.net (8.6.10/950822.1) id JAA27844; Wed, 11 Oct 1995 09:19:03 -0400 Received: from [198.81.225.120] (ppp111.awod.com [198.81.225.120]) by sumter.awod.com (8.6.11/8.6.9) with SMTP id JAA26014; Wed, 11 Oct 1995 09:17:13 -0400 X-Sender: arichon@awod.com Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 11 Oct 1995 09:34:38 +0000 To: chemistry@www.ccl.net From: netsci@awod.com (Network Science) Subject: October issue of Network Science Cc: netsci@awod.com The October issue of NetSci is on-line at: http://www.awod.com/netsci The focus of this issue is bioiniformatics and includes articles by Jay Otero and Hans Sieburg (UCSD), Victor Strelets (Florida State), N. J. Toussant, H. Liu-Johnson and D. Dayton (Chemical Abstracts), George Michaels (George Mason Univ), Ernie Retzel (University of Minnesota) with an editorial page by Michael N. Liebman. In addition to the regular features included in NetSci, the software listing has been significantly expanded. If you or your colleagues have software available and would like to list it in NetSci, please send e-mail to netsci@awod.com From zsyamp01@bastiments.cesca.es Wed Oct 11 09:47:22 1995 Received: from prades.cesca.es for zsyamp01@bastiments.cesca.es by www.ccl.net (8.6.10/950822.1) id JAA27834; Wed, 11 Oct 1995 09:18:54 -0400 Received: from bastiments.cesca.es by prades.cesca.es with SMTP (1.38.193.4/16.2) id AA11375; Wed, 11 Oct 1995 14:16:25 +0100 Received: by bastiments.cesca.es (931110.SGI/930416.SGI) for @prades.cesca.es:chemistry@www.ccl.net id AA01206; Wed, 11 Oct 95 15:21:38 +0200 From: "Alicia Martinez Puebla" Message-Id: <9510111521.ZM1204@bastiments.cesca.es> Date: Wed, 11 Oct 1995 15:21:38 -0600 Return-Receipt-To: "Alicia Martinez Puebla" X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@www.ccl.net Subject: VIJAIE '95 at Barcelona Cc: Albert Palomer Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 VI MEETING ON INDUSTRIAL APPLICATIONS OF ENZYMES ------------------------------------------------ November 29-30 1995 Gallery Hotel, Barcelona, Catalunya, Spain Third Circular and call for papers The Biochemistry and Biotechnology Group of the Associacio de Quimics de l'Institut Quimic de Sarria (A-IQS), invites you to participate in the VI Meeting on Industrial Applications of Enzymes to be held in Barcelona on the 29th and 30th of November 1995. The conference is an European meeting point for all the people related to the world of industrial enzymes. Participants from a wide range of fields including research, marketing and practical applications will gather in Barcelona next November. The meeting is organized in two independent day-sessions to provide the opportunity of selecting the topics of your interest. The first day will be focused on the use of enzymes in the food industry (bakery and flavours) and the second day will be directed to the enzymes in textile industry. A poster session is also scheduled during the meeting. A proceedings book and technical documentation from the Sponsors and Collaborating Companies will be distributed. The III EUROPEAN A-IQS AWARD ON ENZYME TECHNOLOGY will be delivered during the meeting. This award is intended to promote pre-competitive research on innovation of processess or products involving enzyme technology. The meeting is sponsored by the main European enzyme producers, which will also present their last innovations in the industrial applications of enzymes. SCIENTIFIC PROGRAM Lectures in the meeting will be organized as follows: Wednesday, 29 November. 8'45 Registration Session I: Enzymes in the baking industry 9'15 Opening of the Session 9'30 "Advances in the use of enzymes in baking" Dra. Carmen Benedito (Inst. de Agroquimica y Tecnologia de Alimentos-CSIC, Valencia) 10'20 Coffee break 11'00 "New developments of enzymes for the baking industry" Mrs. Joan Qi Si (Novo Nordisk Ferment Ltd.) 11'50 "Enzymes in baking: standardization or functionality?" Dr. Wim van Hartingsveldt (TNO Nutrition and Food Research) 12'40 "Recent progresses in technology and food application of industrial enzymes" Dr. Jerome Souppe (Gist-Brocades) 13'30 Discussion 14'00 End of the morning session 16'30 "Enzymes and their role in bread taste and flavour development" Dra. M. Antonia Martinez-Anaya (Instituto de Agroquimica y Tecnologia de Alimentos- CSIC, Valencia) 17'20 "The taste of DNA" Dr. Albert J.J. van Ooijen (Gist-Brocades) 18'10 "Bread flavour and yeast fermentation technology" Dr. Richard Molard (Institut National de la Recherche Agronomique, INRA, Nantes) 19'00 Discussion 19'30 Closing of the session 21'00 Dinner Thursday, 30 November SessionII: Enzymes in the Textile Industry 8'15 Registration 8'45 Opening of the Session 9'00 "Biotechnological tools in the textile processes" Dr. Ing. Jose Cegarra (Universitat Politecnica de Catalunya, UPC, Terrassa) 9'50 "Enzymatic Big Bang" Dr. Saverio Fornelli (Clariant, Basel) 10'40 Coffee break 11'30 "Wash - performance of a Lipase from Pseudomonas wisconsinensis" Dr. Gerhard Konieckny-Janda (Solvay Enzymes, Brusselles) 12'20 "Biotechnology for ecological textile finishing processes and products" Dr. Wolfgang Kesting (Deutsches Textilforschungszentrum, Krefeld) 13'10 "International cooperation in R+D in the European Union: The Eureka Programme" Dr. Jose M. Gimenez (CDTI, Madrid) 14'00 Discussion 14'30 End of the morning session 16'30 "Applications of enzymes in the textile industry" Mr. Michael G. Schmidt (Novo Nordisk Biotechnologie GmbH) 17'20 "Enzymatic treatment of wool: A possible alternative for dying and finishing" Dra. Asuncion Riba (Universitat Politecnica de Catalunya, UPC, Terrassa) 18'10 Discussion 18'30 III EUROPEAN A-IQS AWARD ON ENZYME TECHNOLOGY "Enzymatic acylation of sucrose as tool to produce potential surfactants" Dr. Antonio Ballesteros (Instituto de Catalisis y Petroleoquimica, CSIC, Madrid) 19'20 Closing of the meeting. Mr. Lluis Segui, President of A-IQS The official languages of the Meeting will be Spanish and English. Simultaneous translation facilities will be available. CONFERENCE VENUE AND ACCOMMODATION INFORMATION The meeting will be held at the Gallery Hotel, located in downtown Barcelona. Sessions will be held in the Hotel and the poster sessions will be in the exhibition foyer outside the exhibition area. A limited amount of accommodation has been reserved at this 4-star hotel with a special rate for the Conference. Please, contact directly the reservation office of the Hotel. Gallery Hotel, Rosellon 249, 08008 Barcelona Tel.: 34 3 4159911, Fax.: 34 3 4159184 REGISTRATION A Registration Form follows. Please, complete the form and return along with the appropriate payment to the Conference Secretariat before November 27th. Registration by fax or e-mail will be accepted if payment is received before November 27th. Places are limited and decision will be made on a first-arrival basis. Full registration entitles participants to the book of Abstracts and attendance at all sessions. Secretary of the Meeting: Associacio de Quimics de l'IQS (A-IQS) Via Augusta 390 08017 Barcelona (Spain) Tel.& Fax: + 34 3 2804276 E-mail: aiqs@iqs.url.es CALL FOR POSTERS Participants are invited to present a poster communication in the poster session that will be opened all along the meeting. The call for papers is opened until October 30st for those willing to present a communication. Instructions are available upon request by fax or e-mail to the Secretariat of the Meeting. All abstracts will be refereed and acceptation will be notified before November 13th. Accepted Abstracts will be published in the proceedings book. Contributions will be included into one of the following topics: - The use of enzymes in food industry and flavour generation. - The use of enzymes in paper and textile industries. - Novel uses of enzymes and new enzymes for industrial applications. - Enzyme technology and process engineering. IMPORTANT DEADLINES Presentation of Abstracts..................Monday, October 30st Notification of accepted Abstracts.........Monday, November 13th Registration and reception of payment......Monday, November 27th SPONSOR COMPANIES AND INSTITUTIONS The Organizing Committee greatefully acknowledges the following Companies for their sponsoring effort: NOVO Nordisk, Gist-Brocades and Solvay Enzymes and for their collaboration to the organization: Acigrasa SA, Biocatalyst Ltd./Gentec SA, Biocon Espagnola SA, Curtex Industrias Sinteticas SA, Laboratorio de Ensayo y Analisis Girona SL, Sapa i Dafa Associes, Tecnufar Iberica SL. Collaboration of the following institutions is also greatfully acknowledged: "Departament de la Presidencia, Direccio General de Recerca i Comissionat per a Universitats i Recerca" of the "Generalitat de Catalunya", "CETS Institut Quimic de Sarria" of the "Universitat Ramon Llull". Please, send the following application form to the Secretary of the Meeting ---------------------------------------------------------------------------- VI MEETING ON INDUSTRIAL APPLICATIONS OF ENZYMES Associacio de Quimics de l'IQS (A-IQS) Via Augusta, 390 08017 Barcelona (Spain) Tel. & Fax AIQS: 34 3 2804276 E-mail aiqs@iqs.url.es 1. DELEGATE NAME AND ADDRESS DETAILS Surame __________________________ First Name _________________________ Position ____________________________________________________________ Affiliation __________________________________________________________ Postal Address ______________________________________________________ Post Code _________________________ City _____________________________ Country ____________________________________________________________ Tel ___________________ Fax __________________ e-mail _________________ 2. ABSTRACTS I wish to submit an Abstract Yes/No. Please, send me the detailed instructions. Poster Title _________________________________________________________ __________________________________________________________________ Authors ___________________________________________________________ 3. DELEGATE REGISTRATION FEES 1 day (29 or 30 November)..................29000PTS* 2 days (29 and 30 November)................44000PTS* * 20% reduction for A-IQS members (1 day: 23000PTS, 2 days: 35200PTS) I wish/donnot wish to attend the meeting Dinner on 29.11.95 (ticket: 6500PTS) Payment to be made in Spanish Pesetas by cheque payable to: "Associacio de Quimics de l'IQS". -------------------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Oct 11 10:54:53 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id KAA00513; Wed, 11 Oct 1995 10:52:59 -0400 Received: from msi.com for Don_Gregory@msi.com by bedrock.ccl.net (8.6.10/950822.1) id KAA13478; Wed, 11 Oct 1995 10:52:57 -0400 Received: from qmail-gw.msi.com by msi.com (4.1/SMI-4.1) id AA09662; Wed, 11 Oct 95 10:47:23 EDT Message-Id: Date: 11 Oct 1995 10:59:30 -0400 From: "Don Gregory" Subject: CHARMm disappearing waters? To: "Comp. Chem. Listserver" X-Mailer: Mail*Link SMTP-QM 3.0.2 Subject: Time:7:32 AM OFFICE MEMO CHARMm disappearing waters? Date:10/11/95 With regards to "disappearing" solvent atoms in a CHARMm run, I can't think of a way this could be happening?!? If the waters were "flying off" as Tom O'Connell suggests, their coordinates wouldn't be "undefined"; but rather very large. I would suggest that Alex send an example input/output file to me (perhaps with the output purged to make it manageable). I'd be happy to have a look, and let eveyone know either what I've found as a subtle suggested change in the input, or perhaps whether this is a new bug. But, there's been enough solvation dynamics run, both in house here, and by users for several years, that I'd think we'd have run into this by now. So, let's see what we can find. Don Gregory ------- Hi Alex, Is it possible that some solvent waters are flying away during the dynamics? Have you tried running the simulation with the quartic droplet potential or using stochastic boundaries? If you think these might help I can give you further details on setup. Cheers, tom ------------------------------------------------------------ Original question: I must thank you all for the help that you have supplied so far. I have a very strange one for you now. I have a quenched dynamics run going on Charmm 22.2, using 15A TIP3 sphere to dissolve methyl- glycoside. I used ABNR to minimise to tolgrd 0.001 and then used a fairly standard quenched dynamics run. The snag is that after 300 steps then program says that some of the atoms have undefined co-ordinates. Has anyone every come across this before. ------------------------------------------ ********************************************** Thomas M. O'Connell, Ph.D. Laboratory for Molecular Modeling School of Pharmacy, CB #7360 University of North Carolina Chapel Hill, NC 27599-7360 phone (919) 966-7821 fax (919) 966-6919 e-mail tmoc@gibbs.unc.edu From owner-chemistry@ccl.net Wed Oct 11 11:54:50 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA01979; Wed, 11 Oct 1995 11:43:51 -0400 Received: from wugate.wustl.edu for reichertd@mirlink.wustl.edu by bedrock.ccl.net (8.6.10/950822.1) id LAA14030; Wed, 11 Oct 1995 11:43:49 -0400 Received: from mirlink.wustl.edu by wugate.wustl.edu (8.6.12/8.6.11) with SMTP id KAA29230 for ; Wed, 11 Oct 1995 10:43:49 -0500 Message-Id: <199510111543.KAA29230@wugate.wustl.edu> Date: 11 Oct 1995 10:43:35 U From: "David Reichert" Subject: GAMESS Question To: "CCL" Dear Netters, I've a question about basis sets and GAMESS that I've been unable to find the answer to. I ran an STO-3G job with 1 diffuse function to handle the anionic charge on a second row transition metal complex. When I look at the Mullikan populations the d orbitals were listed as xx, yy, zz, xy, xz,yz which I thought was how STO3-21G treated d orbitals instead of as zz, xx-yy, xy, xz, yz in STO-3G. Am I mistaken? Any explanation or help would be greatly appreciated. David E. Reichert, Ph.D. Mallinckrodt Inst. of Radiology Div. Radiation Sciences phone: (314)362-8461 fax: (314)362-9940 e-mail: reichertd@mirlink.wustl.edu From VARNAI@ch.bme.hu Wed Oct 11 12:24:50 1995 Received: from ns.bme.hu for VARNAI@ch.bme.hu by www.ccl.net (8.6.10/950822.1) id MAA02774; Wed, 11 Oct 1995 12:19:20 -0400 Received: from ch.bme.hu (ch.bme.hu [152.66.64.1]) by ns.bme.hu (8.6.12/8.6.12) with SMTP id RAA09103 for ; Wed, 11 Oct 1995 17:15:24 +0100 Received: from CH/TEMPQ by ch.bme.hu (Mercury 1.12); Wed, 11 Oct 95 17:28:51 +1100 Received: from TEMPQ by CH (Mercury 1.12); Wed, 11 Oct 95 17:28:26 +1100 From: "Varnai Peter" To: chemistry@www.ccl.net Date: Wed, 11 Oct 1995 17:28:20 GMT+100 Subject: sigma delocalization X-Confirm-Reading-To: "Varnai Peter" X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail v3.22 Message-ID: <4C8161044EC@ch.bme.hu> Hello Cyberchemists, I am involved in a pericyclic reaction mechanism...My question is: What do YOU think about having a TS that is stabilized by sigma aromaticity? Are You aware of any references on this topic? Probably in Prof. Dewar's paper in Mol. Struct. Energ. (1988,6,1-61) there is something about this. Unfortunately, I don't have access to this paper. I hope that You share Your opinions, and I can summarize to all of You! Best to You, Peter Varnai PhD student varnai@ch.bme.hu From raman@bioc01.uthscsa.edu Wed Oct 11 12:33:05 1995 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.10/950822.1) id MAA02735; Wed, 11 Oct 1995 12:16:25 -0400 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Wed, 11 Oct 1995 11:17:10 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA04218; Wed, 11 Oct 95 11:15:52 CDT From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9510111615.AA04218@bioc01.uthscsa.edu> Subject: 3D models of micelles To: chemistry@www.ccl.net Date: Wed, 11 Oct 1995 11:15:52 -0500 (CDT) X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 1624 Has anyone successfully modelled micelles in three dimensions? Any references on this subject would be appreciated. Cheers -raman -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? -Albert Einstein _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From owner-chemistry@ccl.net Wed Oct 11 12:39:51 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id MAA02989; Wed, 11 Oct 1995 12:27:28 -0400 Received: from occam.gh.wits.ac.za for craig@occam.gh.wits.ac.za by bedrock.ccl.net (8.6.10/950822.1) id MAA14545; Wed, 11 Oct 1995 12:27:20 -0400 Received: (from craig@localhost) by occam.gh.wits.ac.za (8.6.12/8.6.9) id SAA08533; Wed, 11 Oct 1995 18:26:16 +0200 Date: Wed, 11 Oct 1995 18:26:16 +0200 (GMT+0200) From: Craig Taverner X-Sender: craig@occam.gh.wits.ac.za To: Taisung Lee cc: chemistry@ccl.net Subject: Re: CCL:PC as a file server? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Taisung, > Our group is looking for a machine as a file server via NFS. We are > considering to buy a high end PC running Linux or WindowsNT. Is there > anybody has experiences about that? We will connect the file server to 3 > IBM RS/6000s and one SGI/R4000. Is there any problem of compatibilty? > Thanks in advance for any reply. We have a network with two linux machines (one 486dx100 16M/1G and on 586dx100 32M/2G) acting as servers to a small network of four Windows for workgroups machines and two other linux machines, roughly speaking (actually all linux machines are partly servers). Sevices provided to the network are file storage, internet e-mail, WWW server, ftp server, Database server (CSDS), computations, all via nfs. It works very well. The pentium server is also being used by remote users on linux, Sun and SGI workstations to very good effect. Considering the domination of unix in the computational field as well as in internetworking, I would recommend linux. It also seems to be very much more efficient (ie. not resource hungry) than it's competitors in the PC market. All networking between linux and other unix machines seems to work very well (we use extensive nfs and remote X11). If your clients are only unix machines, then unix should be your server of choice. If your clients are LAN machines (eg. windows for workgroups). Linux can still be used (as we have with Samba). Cheers, Craig "If God had meant us to be naked, we would have been born that way." Craig Taverner Structural Chemistry, University of the Witwatersrand, South Africa From owner-chemistry@ccl.net Wed Oct 11 15:09:49 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id PAA07993; Wed, 11 Oct 1995 15:05:25 -0400 Received: from msi.com for ryszard@msi.com by bedrock.ccl.net (8.6.10/950822.1) id PAA16198; Wed, 11 Oct 1995 15:05:21 -0400 Received: from aga.msi.com by msi.com (4.1/SMI-4.1) id AA10887; Wed, 11 Oct 95 14:59:47 EDT Received: by aga.msi.com (5.65/DEC-OSF/1-29Feb92); id AA22804; Wed, 11 Oct 1995 15:04:41 -0400 Date: Wed, 11 Oct 1995 15:04:41 -0400 From: ryszard@msi.com (Ryszard Czerminski X 217) Message-Id: <9510111904.AA22804@aga.msi.com> To: Don_Gregory@msi.com, chemistry@ccl.net Subject: Re: CCL:CHARMm disappearing waters? Please note that charmm is using logical function INITIA to determine if coordinates for an atom are defined or not. For this purpose it is comparing X,Y and Z coordinates with a parameter (which is set to 9999.). For this function to return TRUE all three coordinates have to be smaller then 9999. Therefore it is possible to get "undefined" coordinates if some atoms fly far away ( with X > 9999 or Y > 9999 or Z > 9999 ). Note also that "undefined" coordinates will not happen for atoms which fly away in opposite direction i.e. if X < -9999 or Y < -9999 or Z < -9999. I am not quite sure if this is what happens in troubled run, but it is definitely a possibility. Ryszard From elewars@alchemy.chem.utoronto.ca Wed Oct 11 17:24:52 1995 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.10/950822.1) id RAA12119; Wed, 11 Oct 1995 17:24:23 -0400 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.6.10/8.6.10) id RAA13252 for chemistry@www.ccl.net; Wed, 11 Oct 1995 17:24:21 -0400 Date: Wed, 11 Oct 1995 17:24:21 -0400 From: "E. Lewars" Message-Id: <199510112124.RAA13252@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: ELECTRON CORRELATION AND SEMIEMPIRICAL CALCS Re Hank Verhaar's question on whether semiemp heats of form's should get better if electron correlation is include, as is supposed to happen with ab initio. Of course ab in calcs don't give heats of formation directlty; this info' must be coaxed out of them in a roundabout way, usually involving appeal to experimental quantities somewhere. Semiemp methods (some of them anyway) are calibrated against exp to reproduce heats of form'n, so it is not clear why specific electron correlation routines need to be included; indeed, Tim Clark says (A Handbook of Computational Chemistry, 1985, p 97) "An important point to note is that MINDO/3 and MNDO are parametrized at the SCF level to fit experimental results, which already reflect correlation. Therefore any calculations using these methods and considering correlation do not give realistic heats of formation, because {the correlation energy has been included twice, once via the parametrization and once explicitly." Nevertheless, there does seem to be a place for e.g. CI in semiemp methods, e.g. in lowering the energies of transition states to more realistic values as in Thiele's MNDOC. === Errol Lewars ==== From owner-chemistry@ccl.net Wed Oct 11 18:24:53 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id SAA13168; Wed, 11 Oct 1995 18:19:43 -0400 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by bedrock.ccl.net (8.6.10/950822.1) id SAA00567; Wed, 11 Oct 1995 18:19:39 -0400 Received: from bath.ac.uk (actually host mary.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Wed, 11 Oct 1995 23:18:58 +0100 Date: Wed, 11 Oct 1995 23:18:53 +0100 (BST) From: A J Turner To: chemistry@ccl.net Subject: Re: CCL:CHARMm disappearing waters? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! Thank-you for all your help on this matter. My problem is simply sorted out by initialising the velocities correctly! I have not been keeping trajectory files and so cannot be 100% sure that the atoms were lost by going over 999A. However - this would seem likely. Hay - I'm glad to see MSI are on the ball! Cheers to all Alex +--------------------------------------------------+ |Alternate E-mail A.J.Turner@Bath.ac.uk | |www home @ http://www.bath.ac.uk/~chpajt/home.html| +--------------------------------------------------+ From owner-chemistry@ccl.net Wed Oct 11 18:39:51 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id SAA13251; Wed, 11 Oct 1995 18:23:35 -0400 Received: from gusun.acc.georgetown.edu for choic@gusun.acc.georgetown.edu by bedrock.ccl.net (8.6.10/950822.1) id SAA00622; Wed, 11 Oct 1995 18:23:33 -0400 Received: by gusun.acc.georgetown.edu; (5.x/1.1.8.2/6Jan9518:19pm) id AA18002; Wed, 11 Oct 1995 18:19:04 -0400 Date: Wed, 11 Oct 1995 18:19:03 -0400 (EDT) From: Cheol Choi To: chemistry@ccl.net Subject: Transform to redundant internal Coord? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers. I have a simple question. First of all, let me define some terms. X : cartesian displacement coordinate R : internal displacement coordinate If I have N atoms, then I would have 3N of cartesians. Also if I define nun-redundant internal coordinate, I would have 3N-6 or 5 internal coordnate. There is A matrix which transform R into X. X=A*R In general, one could get the inverse (since A is not square matrix, this is not exactly inverse matrix) of A like (Let me use B for inverse of A) A=transpose(B)*inverse(B*transpose(B)) (This formula can only be used for direction independent quantities, such as energy and only hold for nun-redundant internal coordinate.) Now, my problem is this. If I have redundant internal coordinate,which means that there are (is) singularities in B matrix, I could not inverse the B*transpose(B). Therefore I couldn't get the A matrix form B matrix. Gaussian94 uses the redundant internal coordinate to optimize geometry. It actually calculates the hessian matrix in redundant internal coordinate and also gives us the cartesian hessian matrix. So there might be a transformation matrix between these coordinates. Please, let me konw how to get such a transformation matrix. Thank you in advance. Cheol Ho Choi Georgetown Univ. From guest04@montsia.cesca.es Wed Oct 11 19:09:54 1995 Received: from prades.cesca.es for guest04@montsia.cesca.es by www.ccl.net (8.6.10/950822.1) id SAA13712; Wed, 11 Oct 1995 18:55:30 -0400 Received: from montsia.cesca.es by prades.cesca.es with SMTP (1.38.193.4/16.2) id AA13342; Wed, 11 Oct 1995 16:39:26 +0100 Received: by montsia.cesca.es (931110.SGI/911001.SGI) for @PRADES.CESCA.ES:chemistry@www.ccl.net id AA08535; Wed, 11 Oct 95 17:43:20 +0200 Date: Wed, 11 Oct 1995 17:42:30 +0200 (MDT) From: Albert PALOMER Subject: Re: VIJAIE '95 at Barcelona To: Alicia Martinez Puebla Cc: chemistry@www.ccl.net In-Reply-To: <9510111521.ZM1204@bastiments.cesca.es> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hola Alicia, ja he vist que habies enviat el mail a www.ccl.net. Moltes gracies i fins d'aci a una estona. Albert From owner-chemistry@ccl.net Wed Oct 11 19:54:52 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id TAA14671; Wed, 11 Oct 1995 19:54:14 -0400 Received: from rani.chem.yale.edu for lim@rani.chem.yale.edu by bedrock.ccl.net (8.6.10/950822.1) id TAA01071; Wed, 11 Oct 1995 19:54:11 -0400 Received: by rani.chem.yale.edu; Wed, 11 Oct 95 19:54:13 -0400 From: Dongchul Lim Message-Id: <9510112354.AA00407@rani.chem.yale.edu> Subject: 3D molecular structure -> SMILES To: chemistry@ccl.net (Computational Chemistry) Date: Wed, 11 Oct 95 19:54:12 EDT X-Mailer: ELM [version 2.3 PL11] Here is a summary of the replies I got, regarding the conversion program from 3D coord to SMILES. I'd like to thank for the input. -Dongchul Lim, lim@rani.chem.yale.edu [Original Question] > Are there any public domain or free 3D molecular > structure to SMILES translators? ------------------------------------------------------------------------------ From MARTIN%CMDB@randb.pprd.abbott.com Wed Oct 11 12:07:09 1995 Contact Daylight: support@daylight.com. Yvonne Martin Abbott Laboratories ------------------------------------------------------------------------------ From martine@pleiades.chiron.com Wed Oct 11 11:42:47 1995 If you have access to the Daylight toolkit, there are contributed programs for converting mol, pdb, rosdal, and Derwint's WDI formats to smiles. I would be interested in other options as well. Eric Martin martine@chiron.com ------------------------------------------------------------------------------ From wdi@schiele.CHEM.YALE.EDU Wed Oct 11 07:46:48 1995 Yes, but currently without atomic stereochemistry. http://schiele.organik.uni-erlangen.de/cactvs/toolidx.html Dr. Wolf-D. Ihlenfeldt ------------------------------------------------------------------------------ From S.R.Kilvington@soton.ac.uk Wed Oct 11 05:11:55 1995 I have written routines for converting between SMILES and connection tables (going both ways). I can send you the source code (in C) if you want. You'll need to write something to load in your 3D structure files and store them to my connection table format, but that should be fairly easy to do. Simon Kilvington, srk@soton.ac.uk ------------------------------------------------------------------------------ From smb@smb.chem.niu.edu Wed Oct 11 20:24:56 1995 Received: from mp.cs.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.6.10/950822.1) id UAA14911; Wed, 11 Oct 1995 20:11:49 -0400 Received: from cz2.chem.niu.edu by mp.cs.niu.edu with SMTP id AA25418 (5.67b/IDA-1.5 for <@mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@www.ccl.net>); Tue, 10 Oct 1995 10:35:26 -0500 Received: from smb.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA12879; Tue, 10 Oct 95 09:43:30 -0500 Received: by smb.chem.niu.edu (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA21197; Tue, 10 Oct 95 09:42:08 -0500 Date: Tue, 10 Oct 95 09:42:08 -0500 From: smb@smb.chem.niu.edu (Steven Bachrach) Message-Id: <9510101442.AA21197@smb.chem.niu.edu> To: CHEMISTRY@www.ccl.net Subject: ECCC2 Registration Open The Second Electronic Computational Chemistry Conference will take palce from Nov. 1 - 30, 1995. There will be 65 papers covering a wide cross-section of computational chemistry. The conference will be held entirely on the Internet. You can access the conference in two ways. If you do not wish to partake in the discussions, which will be handled by www forms (and not via email), you can get to the conference home page at http://hackberry.chem.niu.edu/ECCC2/homepage.html If you do wish to also participate in the discussions, please register for the conference at http://hackberry.chem.niu.edu/cgi-bin/discuss.cgi This address will also be your entrance into the conference after you register. Please note that the conference officially begins on November 1, 1995. On that date, the full text of the papers will be released. Right now, we are making available only the abstracts. Information on the conference can be obtained at http://hackberry.chem.niu.edu/ECCC2/ Steve Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From CTARG@Levels.UniSA.Edu.Au Wed Oct 11 22:24:54 1995 Received: from Roll.Levels.UniSA.Edu.Au for CTARG@Levels.UniSA.Edu.Au by www.ccl.net (8.6.10/950822.1) id WAA16618; Wed, 11 Oct 1995 22:24:07 -0400 From: Received: from Levels.UniSA.Edu.Au by Levels.UniSA.Edu.Au (PMDF V5.0-4 #9510) id <01HWCOFQ6VC0LODAZ6@Levels.UniSA.Edu.Au> for chemistry@www.ccl.net; Thu, 12 Oct 1995 11:53:22 +0930 Date: Thu, 12 Oct 1995 11:53:22 +0930 Subject: potential energy of a bond? To: chemistry@www.ccl.net Message-id: <01HWCOFQ8QUQLODAZ6@Levels.UniSA.Edu.Au> X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hi, I think this is rather a trivial question but never mind. I'd like to know how potential energy of a bond length or bond angle is calculated. The reason for this enquiry is that we want to calculate force field parameters from semi-empirical or ab-intio calculations. I thought that one possiblity is to take a known molecular structure and vary one aspect of it. For example shrink and stretch a bond length and from this calculate a energy/Angstrom force constant. Is this approach sensible or is there an easier way? Thanks Andy From zhangqy@infoc3.icas.ac.cn Wed Oct 11 22:33:14 1995 Received: from infoc3.icas.ac.cn for zhangqy@infoc3.icas.ac.cn by www.ccl.net (8.6.10/950822.1) id WAA16600; Wed, 11 Oct 1995 22:20:27 -0400 Received: (from zhangqy@localhost) by infoc3.icas.ac.cn (8.6.9/8.6.9) id IAA00185; Tue, 10 Oct 1995 08:02:38 +0800 Date: Tue, 10 Oct 1995 08:02:38 +0800 From: Zhang Qiyuan Subject: CCL:G:question about the setting up G92W/DFT for windows To: chemistry@www.ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! CCL's: I am puzzled by a question and hope to get your help. We bought the software 'G92W/DFT for windows'. This software is designed for the seting up in PC 486, and that is only an exectuablly binary code. We set up in PC486 and work well. Now, We want to set up in pentrium in place of in PC486. Once the program began to work in pentrium, it keeps in reading data from the input file even when the input file is the test file. I have asked the gaussian company, but no response. Who can give me any suggestion? All messages are warmly welcome. Thank you in advance for your reply. sincerely, Guo, Jian-Xing ******************************************************************** * Guo, Jian-xing * * PH.D. student * * Institute of Chemistry, Acadeia Sinica * * Beijing 100080 * * P. R. CHINA * * E-mail: zhangqy@infoc3.icas.ac.cn * ********************************************************************