From Jeffrey.Gosper@brunel.ac.uk Wed Oct 25 05:14:14 1995 Received: from monge.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.6.10/950822.1) id FAA23160; Wed, 25 Oct 1995 05:12:48 -0400 Received: from chem-pc-18.brunel.ac.uk by monge.brunel.ac.uk with SMTP (PP) id <05340-0@monge.brunel.ac.uk>; Wed, 25 Oct 1995 09:12:17 +0000 Date: Wed, 25 Oct 1995 09:12:12 BST From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: M:Trying to pereform IRC calculations To: CHEMISTRY@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII A few days ago I requested information about the output from IRC calculations within MOPAC6. Thanks to all those that provided the answer. The level of output from an IRC is controlled by a number of keywords but an essential one for getting geoemtires printed (and is not mentioned in the IRC section of MOPACs manual) is the keyword LARGE. This is true in both MOPAC6 and MOPAC93. Combining LARGE with X-PRIO in IRC calculations produces the output I desire. PS: The output produced from these calculations can be very large and I'm working towards a program that automatically constructs a multistructure XYZ file from the output. Such an XYZ file can be visualized/analysed using XMOL or my program Re_View. Thanks again to all those who helped. /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ 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://http2.brunel.ac.uk:8080/~castjjg \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From Poehlmann@rus.uni-stuttgart.de Wed Oct 25 07:14:11 1995 Received: from artemis.rus.uni-stuttgart.de for Poehlmann@rus.uni-stuttgart.de by www.ccl.net (8.6.10/950822.1) id HAA24282; Wed, 25 Oct 1995 07:04:14 -0400 Received: from awshp.rus.uni-stuttgart.de (awshp.rus.uni-stuttgart.de [129.69.29.181]) by artemis.rus.uni-stuttgart.de with ESMTP id MAA16185 (8.6.12/IDA-1.6); Wed, 25 Oct 1995 12:04:03 +0100 Received: by awshp.rus.uni-stuttgart.de (940816.SGI.8.6.9/BelWue-1.0SG(subsidiary)) (for ) id LAA14094; Wed, 25 Oct 1995 11:04:01 GMT Message-Id: <199510251104.LAA14094@awshp.rus.uni-stuttgart.de> Subject: Supercomputer Usage in Chemical Industry To: chemistry@www.ccl.net Date: Wed, 25 Oct 95 12:04:00 MEZ From: "Dr. Heinz Poehlmann" X-Mailer: ELM [version 2.3 PL11] Hi there, I am looking for information about supercomputer usage in chemical and pharmaceutical industry worldwide. Any hints welcome. Thanks, Heinz .-------------------------------------------------------------------------. | Dr. Heinz W. Poehlmann Regionales Rechenzentrum | | Manager Applications Department der Universitaet Stuttgart | | Computational Chemistry Support (University Computer Center) | | phone: (49)-711-685-5992 Allmandring 30 | | fax: (49)-711-6787626 D-70550 Stuttgart | | e-mail: poehlmann@rus.uni-stuttgart.de Germany | '-------------------------------------------------------------------------' From owner-chemistry@ccl.net Wed Oct 25 08:59:13 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id IAA25435; Wed, 25 Oct 1995 08:52:57 -0400 Received: from maingate.ki.se for ae@thon.csb.ki.se by bedrock.ccl.net (8.6.10/950822.1) id IAA25698; Wed, 25 Oct 1995 08:52:54 -0400 Received: from thon.csb.ki.se by maingate.ki.se (5.61+IDA/KTH/LTH/Ultrix3.0-C) id AAmaingate.ki.se28197; Wed, 25 Oct 95 11:53:49 -0100 Posted-Date: Wed, 25 Oct 1995 13:55:17 +0100 Received: from skua.csb.ki.se by thon.csb.ki.se (4.1/SMI-4.1) id AA06623; Wed, 25 Oct 95 14:02:43 +0100 From: ae@thon.csb.ki.se (Arne Elofsson) Received: by skua.csb.ki.se; (5.65/1.1.8.2/13Jan95-0346PM) id AA05438; Wed, 25 Oct 1995 13:55:17 +0100 Date: Wed, 25 Oct 1995 13:55:17 +0100 Message-Id: <9510251255.AA05438@skua.csb.ki.se> To: CHEMISTRY@ccl.net In-Reply-To: haney@netcom.com's message of Tue, 24 Oct 1995 10:47:47 -0700 (PDT) Subject: Re: CCL:Folding References: <199510241747.KAA28358@netcom11.netcom.com> In article <199510241747.KAA28358@netcom11.netcom.com> haney@netcom.com (Dr. David N. Haney) writes: > > Antonio Rosato writes: > > here is my question: is there a program that allows one to fold a protein > > of which only the sequence is known, on the basis of the folding of > > a similar one? How high should be the omology of the two? > I would say if you have 30% sequence identity it is trivial, between 20 % and 30% you should be able to get it mostly correct, while with less than 20% it is difficult. > You should have a look at George Rose's recent work: > > Srinivasan and Rose, Proteins, 22:81-99 (1995) > Nichols, Rose, Ten Eyck and Zimm, Proteins, 23:38-48 (1995) > Yes, and ofcourse this works very well, and all my crystallogaphic friends just quit their jobs. :> There was an quite interesting discussion about G. Roses methods in bionet.proteins, I guess if anyone is interested they can look it up in the bionet archives, (search for folding, rose, linus). I guess the conclusion was that, interesting method that works surprisingly well (on a small test set) for secondary (and some super- secondary) structure prediction, but does not predict anything about tertiary structures. arne (To think before you speak is as to wipe your ass before you shit.) ----------------------------------------------------------------- From: Arne Elofsson Email: arne@biokemi.su.se WWW: http://www.doe-mbi.ucla.edu/people/arne/main.html From moralega@a1.lldmpc.umc.dupont.com Wed Oct 25 10:29:14 1995 Received: from gatekeeper.es.dupont.com for moralega@a1.lldmpc.umc.dupont.com by www.ccl.net (8.6.10/950822.1) id KAA27655; Wed, 25 Oct 1995 10:17:11 -0400 Received: by gatekeeper.es.dupont.com; id AA02406; Wed, 25 Oct 95 10:17:04 -0400 Received: by esds01.es.dupont.com; id AA11147; Wed, 25 Oct 95 10:17:00 -0400 Received: from umc by esds01.es.dupont.com via MR/ESVAX with conversational-MRIF;Wed, 25 Oct 95 10:17:00 -0400 Posted: Wed, 25 Oct 95 10:02:01 -0400 Date: Wed, 25 Oct 95 09:57:23 -0400 Sender: moralega@a1.lldmpc.umc.dupont.com From: "GUILLERMO A. MORALES" Message-Id: <01700152015991/744035@LLDMPC> App-Message-Id: To: chemistry@www.ccl.net Subject: Wizard program. Msg-Class: ALL-IN-1 IOS Server for OpenVMS V3.1 BL121 (US) ENGLISH 17-JUN-1994 [This message is converted from WPS-PLUS to ASCII] Dear netters, Could anybody please tell me where I could find a program called wizard? I know its developer is Pat Walters and that the program has applications in the area of combinatorial chemistry. Thanks a lot in advance. Guillermo A. Morales E-mail: moralega@lldmpc.dnet.dupont.com From nervi@chpc06.ch.unito.it Wed Oct 25 12:44:16 1995 Received: from chpc06.ch.unito.it for nervi@chpc06.ch.unito.it by www.ccl.net (8.6.10/950822.1) id MAA01644; Wed, 25 Oct 1995 12:38:08 -0400 Received: (from nervi@localhost) by chpc06.ch.unito.it (8.6.9/8.6.9) id RAA14531; Wed, 25 Oct 1995 17:47:57 +0100 Date: Wed, 25 Oct 1995 17:47:55 +0100 From: Carlo Nervi Subject: Best Fitting Algorithms To: chemistry@www.ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, I'm interested in your opinions about various best fitting algorithms for non-linear optimization. Output of my program (an electrochemical simulator) is a wave (couple of calculated points) which must be compared with experimental data. Actually I'm using a modified Simplex algorithm [1-2], but I'm afraid that something better could be applied. The simulation is quite time-consuming, so I should minimize calls to function. Error evaluation should not require further call to the function. Thank you, Carlo Nervi [1] J.A.Nelder, R.Mead, Comput.J., 7 (1965) 308. [2] P.B.Ryan, R.L.Barr, H.D.Todd, Anal.Chem., 52 (1980) 1460. ---------------------------------------------------------------------------- Carlo Nervi Dipartimento di Chimica Inorganica, Chimica Fisica e Chimica dei Materiali, via P. Giuria 7, 10125 Torino, ITALY phone: (Italy)-11-6707508 | e-mail: nervi@chpc06.ch.unito.it fax: (Italy)-11-6707855 | nervi@silver.ch.unito.it http://chpc06.ch.unito.it/ ---------------------------------------------------------------------------- From stoutepf@carbon.dmpc.com Wed Oct 25 13:46:47 1995 Received: from gatekeeper.es.dupont.com for stoutepf@carbon.dmpc.com by www.ccl.net (8.6.10/950822.1) id NAA03478; Wed, 25 Oct 1995 13:38:21 -0400 Received: by gatekeeper.es.dupont.com; id AA19459; Wed, 25 Oct 95 13:38:20 -0400 Received: by esds01.es.dupont.com; id AA28453; Wed, 25 Oct 95 13:38:08 -0400 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Organization: The DuPont Merck Pharmaceutical Company X-Mailer: Eudora Pro 2.1.3 for Macintosh X-Url: http://www.halcyon.com/stouten/index.html Date: Wed, 25 Oct 1995 13:39:36 -0400 To: "GUILLERMO A. MORALES" From: stoutepf@carbon.dmpc.com (Pieter Stouten) Subject: Re: CCL:Wizard program. Cc: chemistry@www.ccl.net Hi Guillermo, Pat Walters is now at Vertex. Yesterday, I hosted his boss Mark Murcko who gave a presentation here at DMPC in our Computational Chemistry Seminar Series. We also had a round table discussion where the continued development of Wizzard was touched upon. Pity you missed him. If Pat Walters does not respond to your mail himself, please contact Mark Murcko (markm@portal.vpharm.com) or Ajay to obtain his email address. Good luck, Pieter. -- ** Note that my e-mail address has changed once again. I hope it will not ** ** happen again soon. Please use stoutepf@carbon.dmpc.com from now on. ** Pieter Stouten || Nothing shocks me; Computer Aided Drug Design Group || The DuPont Merck Pharmaceutical Company || I am a scientist! P.O. Box 80353, Wilmington, DE 19880-0353 || Phone: +1 (302) 695 3515 || -- Fax: +1 (302) 695 2813 || Internet: stoutepf@carbon.dmpc.com || Indiana Jones From fparnold@structures.uchicago.edu Wed Oct 25 14:14:17 1995 Received: from midway.uchicago.edu for fparnold@structures.uchicago.edu by www.ccl.net (8.6.10/950822.1) id NAA04334; Wed, 25 Oct 1995 13:59:45 -0400 Received: from structures.uchicago.edu (structures.uchicago.edu [128.135.44.4]) by midway.uchicago.edu (8.6.10/8.6.4) with ESMTP id MAA02546 for <@midway.uchicago.edu:chemistry@www.ccl.net>; Wed, 25 Oct 1995 12:59:45 -0500 Received: by structures.uchicago.edu (940816.SGI.8.6.9/940406.SGI) for chemistry@www.ccl.net id MAA03287; Wed, 25 Oct 1995 12:39:05 -0500 Date: Wed, 25 Oct 1995 12:39:05 -0500 From: fparnold@structures.uchicago.edu (Fred P. Arnold) Message-Id: <199510251739.MAA03287@structures.uchicago.edu> To: chemistry@www.ccl.net Subject: TB-LMTO v 4.6 Greetings: We have recently obtained TB-LMTO (V. 4.6, Dec 1994) from the authors and have run into some difficulties in installation. On an RS/6k running AIX 3.2.5 an error in the atomic section of the code occurs when running lmhart.run, which reports that the wrong number of nodes are in the solution to an orbital. The error seems to be in the routine rsq1, which is the subroutine which incorrectly reports the number of nodes. Has anybody else who uses this package run into this problem, or have suggestions on alleviating it? -fred fparnold@structures.uchicago.edu From zsysmh01@falco.cesca.es Wed Oct 25 04:35:36 1995 Received: from prades.cesca.es for zsysmh01@falco.cesca.es by www.ccl.net (8.6.10/950822.1) id EAA22563; Wed, 25 Oct 1995 04:35:34 -0400 Received: from falco.cesca.es by prades.cesca.es with SMTP (1.38.193.4/16.2) id AA23834; Wed, 25 Oct 1995 09:33:16 +0100 Received: by falco.cesca.es (931110.SGI/911001.SGI) for @prades.cesca.es:chemistry@www.ccl.net id AA19711; Wed, 25 Oct 95 10:38:22 +0200 From: "Sara MOYA" Message-Id: <9510251038.ZM19709@falco.cesca.es> Date: Wed, 25 Oct 1995 10:38:21 -0600 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@www.ccl.net Hello, I tried to install the DENSITY program (it is an electron-density plotting program wich comes with MOPAC93) for a Silicon Graphics and I had problems when I run it (core dumped and I can't see any graphic) I think the problem is the interface betwen FORTRAN77 and graphic routine, if someone know the e-mail of the author, please send me a mail to smoya@cesca.es Thank you. Sara/ From rcfort@maine.maine.edu Tue Oct 24 11:52:39 1995 Received: from MAINE.maine.edu for rcfort@maine.maine.edu by www.ccl.net (8.6.10/950822.1) id LAA05234; Tue, 24 Oct 1995 11:52:38 -0400 Date: Tue, 24 Oct 1995 11:52:38 -0400 Message-Id: <199510241552.LAA05234@www.ccl.net> Received: from rfort3.umeche.maine.edu by MAINE.maine.edu (IBM VM SMTP V2R3) with TCP; Tue, 24 Oct 95 11:51:12 EDT X-Sender: rcfort@maine.maine.edu (Unverified) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: rcfort@maine.maine.edu (Raymond C. Fort, Jr.) Subject: X-Windows Clients and Molecular Modeling I have recently received an NSF-ILI grant for the purchase of SGI workstations that will be used to introduce molecular modeling into the undergraduate and graduate curricula. Our plan is to run SPARTAN, PCModel, and MacroModel on the workstations; all are available as X-applications. Then we will provide student access from a Department PC cluster by running X-terminal emulators on the PCs. I would be interested to hear from persons who have successfully applied this kind of connectivity to modeling software, even if it did not involve the specific programs cited. What X-term software is best? (We currently are looking at PC-Xware from NCD and XoftWare from Age). What problems did you encounter? Since this could generate considerable bandwidth, please e-mail directly to me and I will summarize for the list. Thanks. Professor Ray Fort, Jr. Voice: (207)-581-1180 Department of Chemistry FAX: (207)-581-1191 University of Maine E-mail: rcfort@maine.maine.edu Orono ME 04469 rfortjr@fort.umeche.maine.edu Computational organic chemistry, especially on wood- and paper-related problems From haney@netcom.com Tue Oct 24 13:51:23 1995 Received: from netcom11.netcom.com for haney@netcom.com by www.ccl.net (8.6.10/950822.1) id NAA07510; Tue, 24 Oct 1995 13:51:21 -0400 Received: by netcom11.netcom.com (8.6.12/Netcom) id KAA28358; Tue, 24 Oct 1995 10:47:48 -0700 From: haney@netcom.com (Dr. David N. Haney) Message-Id: <199510241747.KAA28358@netcom11.netcom.com> Subject: Re: CCL:Folding To: antonio@risc1.lrm.fi.cnr.it (Antonio Rosato) Date: Tue, 24 Oct 1995 10:47:47 -0700 (PDT) Cc: CHEMISTRY@www.ccl.net Antonio Rosato writes: > here is my question: is there a program that allows one to fold a protein > of which only the sequence is known, on the basis of the folding of > a similar one? How high should be the omology of the two? You should have a look at George Rose's recent work: Srinivasan and Rose, Proteins, 22:81-99 (1995) Nichols, Rose, Ten Eyck and Zimm, Proteins, 23:38-48 (1995) -- ************** David N. Haney, Ph.D. **************** * Haney Associates Phone - 619-566-1127 * * 12010 Medoc Ln. * * San Diego, CA 92131 Fax - 619-586-1481 * ************** Email - haney@netcom.com *************** From owner-chemistry@ccl.net Wed Oct 25 08:44:03 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id IAA25220; Wed, 25 Oct 1995 08:44:02 -0400 Received: from pimaia2w.prodigy.com for GMFL76A@mail.prodigy.com by bedrock.ccl.net (8.6.10/950822.1) id IAA25650; Wed, 25 Oct 1995 08:43:59 -0400 Received: from mail.prodigy.com ([199.4.137.13]) by pimaia2w.prodigy.com (8.6.10/8.6.9) with SMTP id IAA36868 for ; Wed, 25 Oct 1995 08:35:42 -0400 Date: Wed, 25 Oct 1995 08:22:53 EDT From: GMFL76A@prodigy.com (DR ARUP K GHOSE) X-Mailer: PRODIGY Services Company Internet mailer [PIM 3.2-342.56] Message-Id: <013.03535424.GMFL76A@prodigy.com> To: chemistry@ccl.net Subject: Announcement: LibCom AM Technologies Inc. announces the release of their combinatorial library builder and analyzer program LibCom along with Galaxy Version 2.1: A general purpose molecular modeling and drug design package for Silicon Graphics and IBM workstations. The current capabilities of LibCom along with the other modules of Galaxy are: (i) Build physically realistic 3D-structures of either a combinatorial chain or a substitution case. (ii) Calculate several key physicochemical properties of the whole library to create a standard Galaxy 3D structure/property database. (iii) Analyze properties to estimate the distribution and diversity of the library. (iv) Search compounds satisfying property range, 3D-pharmacophore geometry, substructure, title etc. (v) Develop a QSAR and apply it for an automated prediction on the database. For more information contact: AM Technologies Inc., 210-677-8200; Fax 210-677-0335; e-mail amucs@aol.com From carol@still3.chem.columbia.edu Tue Oct 24 16:44:09 1995 Received: from mailhub.cc.columbia.edu for carol@still3.chem.columbia.edu by www.ccl.net (8.6.10/950822.1) id QAA12457; Tue, 24 Oct 1995 16:44:05 -0400 Received: from still3.chem.columbia.edu by mailhub.cc.columbia.edu with SMTP id AA03339 (5.65c+CU/IDA-1.4.4/HLK for <@mailhub.cc.columbia.edu:chemistry@www.ccl.net>); Tue, 24 Oct 1995 16:14:55 -0400 Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for @mailhub.cc.columbia.edu:chemistry@www.ccl.net id AA14862; Tue, 24 Oct 95 16:14:55 -0400 Date: Tue, 24 Oct 95 16:14:55 -0400 From: carol@still3.chem.columbia.edu (Carol Parish) Message-Id: <9510242014.AA14862@still3.chem.columbia.edu> Subject: MacroModel UserGroup needs Listserv Administrator To: chemistry@www.ccl.net Dear Netters, The MacroModel development group is looking for someone to administer the MacroModel user mailing list, mmodinfo. Doug Smith had been doing this, but Doug is no longer at the University of Toledo, and the list has been discontinued as a result. The purpose of mmodinfo is to provide an independent forum for exchange of questions, answers, complaints, kudos, suggestions and discussions concerning the MacroModel/BatchMin/XCluster software. In keeping with the concept of this list as primarily by and for MacroModel users, we'd like it to be administered by a member of the user community. We would be happy to assist with setting up the list. Anyone volunteering should bear in mind that to administer the list successfully will require a small but continuous outlay of time -- perhaps an hour or so per week. Anyone interested in volunteering should contact us at mmod@still3.chem.columbia.edu. We'd also like to take this opportunity to thank Doug Smith for carrying out this responsibility for several years. Regards, Carol Parish ==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+=== Carol Parish Ph.D. Department of Chemistry carol@still3.chem.columbia.edu Columbia University (212) 854-5143 New York, NY 10027 (718) 981-0356 ==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+=== From istvan@bioorg.ee.cua.edu Wed Oct 25 18:29:20 1995 Received: from pluto.ee.cua.edu for istvan@bioorg.ee.cua.edu by www.ccl.net (8.6.10/950822.1) id SAA11423; Wed, 25 Oct 1995 18:22:27 -0400 From: Received: from bioorg.ee.cua.edu (bioorg.ee.cua.edu [136.242.140.81]) by pluto.ee.cua.edu (8.6.12/8.6.9) with ESMTP id SAA25002 for <@pluto.ee.cua.edu:chemistry@www.ccl.net>; Wed, 25 Oct 1995 18:15:57 -0400 Received: by bioorg.ee.cua.edu (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id SAA14796; Wed, 25 Oct 1995 18:25:44 -0400 Message-Id: <9510251825.ZM14794@bioorg.ee.cua.edu> Date: Wed, 25 Oct 1995 18:25:40 -0400 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: program information Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Netters, I am looking for a program wich have the following features: - can calculate the equation of the plane defined by the coordinates of 3 atoms; - can find the distance from an atom to the plane defined above; - the program runs on PC or Macintosh. Thanks for every help. Istvan Enyedy istvan@bioorg.ee.cua.edu From owner-chemistry@ccl.net Wed Oct 25 21:14:23 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id VAA14079; Wed, 25 Oct 1995 21:01:25 -0400 Received: from bioc1.biosym.com for david@iris35.biosym.com by bedrock.ccl.net (8.6.10/950822.1) id VAA02481; Wed, 25 Oct 1995 21:01:22 -0400 Received: from iris35.biosym.com by bioc1.biosym.com (5.64/0.0) id AA20663; Wed, 25 Oct 95 17:59:28 -0700 Received: by iris35.biosym.com (940816.SGI.8.6.9/930416.SGI) id SAA12582; Wed, 25 Oct 1995 18:00:35 -0700 Date: Wed, 25 Oct 1995 18:00:35 -0700 From: david@iris35.biosym.com (David Rigby) Message-Id: <199510260100.SAA12582@iris35.biosym.com> To: chemistry@ccl.net Subject: MRS 4-day Modeling Symposium Reminder Cc: david@iris35.biosym.com ***REMINDER***REMINDER***REMINDER***REMINDER***REMINDER***REMINDER***REMINDER*** Next year's spring MRS meeting will feature a 4-day symposium focusing on the current state-of-the-art in computational modeling of ceramics, metals and polymers (and any combinations of the above!). The meeting will be held in the San Francisco Marriott from April 8-12. All abstracts should be submitted to the MRS using either email, mail, fax, or the WWW by November 1. To request templates and/or submit abstracts contact the MRS by either of the following routes: email: s96@abstracts.mrs.org www: Direct submission via the web, see http://www.mrs.org (URL for meeting page is http://dns.mrs.org/meetings/spring96/CFPFB.S96.html) Mail: Send the completed abstract template from the July mailing of the MRS 1996 Spring Meeting Call For Papers booklet to: Abstract Enclosed Materials Research Society 9800 McKnight Road Pittsburgh, PA 15237 Fax: Fax the completed abstract template from the July mailing of the MRS 1996 Spring Meeting Call For Papers booklet to: (412) 367-4373 Questions regarding the actual program can be directed to organizers G. Ceder (Ceramics and Metals) and D. Rigby or B. Eichinger (Polymers). We look forward to receiving your abstract and to seeing you in San Francisco! With Best Wishes The "Symposium W" organizers. ------------------------------------------------------------------------------ SYMPOSIUM W: COMPUTATIONAL MATERIALS SCIENCE - STRUCTURAL, MECHANICAL AND TRANSPORT PROPERTIES Modeling the behavior of advanced materials systems, containing ceramics, metals and polymers, frequently requires the use of computational techniques spanning a vast range of length and time scales. Moreover, there is increasing interest in using properties calculated for a system at short length scales as input to calculations performed at longer length scales. This symposium will aim to provide a forum for researchers whose work involves ceramics, metals, or polymers to discuss the many facets of materials property modeling. The symposium is organized into four major sessions, focusing on electronic structure and energy methods, atomistic modeling, mesoscopic systems, and continuum methods. Contributions describing newly-developed simulation algorithms and methodologies are welcomed, in addition to papers dealing with applications to systems of technological interest. Papers focusing on the following areas are encouraged: - Use of quantum methods for developing atomistic forcefield parameters - Use of quantum methods for direct structure prediction - Approaches suitable for quantum and atomistic modeling of systems comprising combinations of inorganic, metallic and organic components (e.g. embedded atom methods, unified forcefields) - Atomistic simulation methods for investigation of - Mechanical Properties (elastic constants, yielding, creep, fracture, dislocations) - First principles prediction of phase stability in solids - Liquid-liquid phase separation - Systems containing interfaces (composites, coatings) - Transport phenomena (diffusion, shear viscosity, thermal conductivity) - Coarse-grained methods (e.g. integral equation theories) - General methods available for simulation of mesoscopic systems (colloidal behavior/flow of suspensions). - Modeling of microstructural evolution - Properties of anisotropic materials; aggregate models - Prediction of residual stress, strain and cracking, interfacial fracture toughness Potential contributors' attention is drawn to two related symposia - symposium S "Aqueous Chemistry and Geochemistry of Oxides, Oxyhydroxides and Related Materials", and symposium Y "Non-Classical Structure-Controlled Macromolecules (dendrimers)". Partial list of invited speakers: D. Pettifor (Oxford, UK), D. Vanderbilt (Rutgers), C. Van de Walle (Xerox), R. Jaffe (NASA), B. Burton (NIST), S. Foiles (Sandia National Laboratories), D. Srolovitz (Michigan), U. Suter (ETH, Zurich), C. Wolverton (NREL), A. Balazs (Pittsburgh), E. Nauman (RPI), H. Frost (Dartmouth), R. Phillips (Brown Univ.), I. Ward (Leeds, UK). Symposium Organizers Gerbrand Ceder Room 130-5041 Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge, MA 02139 Phone: (617) 253-1581 Fax: (617) 252-1020 email: gerd@lanai.mit.edu James R. Chelikowsky Department of Chemical Engineering University of Minnesota 421 Washington Avenue SE Minneapolis, MN 55455 Phone: (612) 625-4837 Fax: (612) 626-7246 email: jrc@msi.umn.edu Bruce E. Eichinger Biosym Technologies, Inc. 9685 Scranton Road San Diego, CA 92121 Phone: (619) 546-5540 Fax: (619) 458-0136 email: bruce@biosym.com Kim F. Ferris K2-44 Pacific Northwest Laboratory P.O. Box 999 Richland, WA 99352 Phone: (509) 375-3754 Fax: (509) 375-2186 email: kim@darter.pnl.gov David Rigby Biosym Technologies, Inc. 9685 Scranton Road San Diego, CA 92121 Phone: (619) 546-5596 Fax: (619) 458-0136 email:david@biosym.com ------------------------------------------------------------------------------ -- From owner-chemistry@ccl.net Wed Oct 25 21:29:23 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id VAA14629; Wed, 25 Oct 1995 21:27:40 -0400 Received: from chamber.cco.caltech.edu for tmmec@fcindy5.NCIFCRF.GOV by bedrock.ccl.net (8.6.10/950822.1) id VAA02688; Wed, 25 Oct 1995 21:27:38 -0400 Received: from gap.cco.caltech.edu by chamber.cco.caltech.edu with ESMTP (8.6.12/DEI:4.41) id SAA23457; Wed, 25 Oct 1995 18:27:38 -0700 Received: from fcindy5.NCIFCRF.GOV by gap.cco.caltech.edu with ESMTP (8.6.7/DEI:4.41) id SAA23967; Wed, 25 Oct 1995 18:27:35 -0700 Received: by fcindy5.NCIFCRF.GOV (940816.SGI.8.6.9/930416.SGI.AUTO) for MLIST-CHEMISTRY@NNTP-SERVER.CALTECH.EDU id VAA08299; Wed, 25 Oct 1995 21:27:58 -0700 Date: Wed, 25 Oct 1995 21:27:58 -0700 From: tmmec@fcindy5.NCIFCRF.GOV (tmmec) Message-Id: <199510260427.VAA08299@fcindy5.NCIFCRF.GOV> To: MLIST-CHEMISTRY@NNTP-SERVER.CALTECH.EDU Subject: TMMeC - Call for Papers Dear Colleagues, The Molecular Modeling e-Conference (TMMeC), a new mechanism for the publication of scientific papers which blends together the benefits of a Scientific Meeting, a printed paper and a multimedia publication, is making through this means its first CALL-FOR-PAPERS. Organized primarily in the Internet, the TMMeC displays the multimedia works of participating authors in three mirror sites, located in USA, Europe and Latin-America. The electronic addresses of these sites are http://bilbo.edu.uy/agora http://uqbar.ncifcrf.gov/agora http://stark.udg.es/agora The conference takes advantage of the posibilities of the WWW and the Chemical Mime Types by providing the authors with unmatched freedom for the communication of their ideas. In TMMeC the readers will have the opportunity to comment about the ideas of other authors, adding their own comments to a special section of each paper. Thus, the usual verbal exchange produced in normal scientific meetings is preserved, with the advantage that even those scientists not involved in the discussions can benefit from the conclusions. The open discussion of the papers would also serve as a means to ensure the highest quality of material is exposed in the e-Conference. The products of the e-Conference are permanent in time. Not only the whole multimedia version of the papers will be produced in CD-ROM but also a printed copy of the work will be produced, if the authors wish so, by choosing for this purpose one of the journals that have agreed to be associated with us in this venture. One of the main characteristics of this conference is that we are not limiting it to works published in English. In fact, it will bring the opportunity to scientist of Latin expression to obtain accelerated publications in their native languages. This characteristic will also be used to give support to the Congresses of Theoretical Chemists of Latin Expression and their Association, just formed in Spain. A second unique characteristic is that we will be publishing not only contributed papers, but Current Reviews of interest to the Theoretical Chemistry and Molecular Modeling community. Differently from their printed analogs, Current Reviews, only present in the e-Conference, will be continuously updated. Even at the same moment that a new contribution is produced in the field. This can be accomplished using the automatic facilities that only an electronic publication may offer. These reviews promise to be a highest impact publication as they would become a necesary entry point for anyone looking for up to day information in any of the subjects covered in them. All these exciting projects and others are fully described in the editorial pages of the conference and we will be extremely pleased if you visit TMMeC. You will find there a more detailed description about the scope of our ideas. We apologize for any duplications of this letter that may reach your mail-box. This first and only Call for Papers is being send to several especialized mail lists, thus duplications may occur. With our best regards, Oscar N. Ventura (oscar@bilbo.edu.uy) Raul E. Cachau (cachau@ncifcrf.gov) Miquel Duran (quel@stark.udg.es) From kmay@trans.net Wed Oct 25 16:59:29 1995 Received: from ns.trans.net for kmay@trans.net by www.ccl.net (8.6.10/950822.1) id QAA10109; Wed, 25 Oct 1995 16:59:26 -0400 Received: from by ns.trans.net (4.1/SMI-4.1) id AB15692; Wed, 25 Oct 95 22:55:48 BST Message-Id: <9510252155.AB15692@ns.trans.net> X-Sender: kmay@mailhost Date: Wed, 25 Oct 1995 23:03:13 +0200 To: CHEMISTRY@www.ccl.net From: kmay@trans.net (Klaus J.W.May) Subject: CCL:Folding >Date: Wed, 25 Oct 1995 22:43:33 +0200 >From:kmay@trans.net (Klaus J.W.May) >Subject:Re: CCL:Folding > >>Dear Netters, >> >>here is my question: is there a program that allows one to fold a protein >>of which only the sequence is known, on the basis of the folding of >>a similar one? How high should be the omology of the two? >> >>My actual problem is: I have the sequence of a protein, but no x-ray nor >>NMR structure is available, and I would like to do dynamics and/or >>modeling on that. >>As usual, any suggestion is welcome. Thank you. >>Cheers, >>Antonio > >Owtch, > >dear Antonio, > >a complicated problem! If one could give you the final answer, he/she is >probably a good candidate for the Nobel price. >You can approach the problem gradually. Are there other structures (Xray) >known of proteins with functional homology? Then you could go with Biosym's >Homology Program or use Eisenberg's approach. Or look at George Rose's recent Papers in" Proteins" Are there clear secondary structural domains ( there are many programs around, which do that analysis - some better, some worse - it's mainly a function of the scoring matrix)? >You can use those motifs to proceed gradually into larger arrangements - >always with a close eye on known structures ( have a look at Articles from >Jane and Dave Richardson). Probably you'll start with Polyalanine and take >care of the sidechaines later. Lucky one, when you have defined disulfides in >your structure - this alrady helps a lot. > >An excellent program to help you to interacively model motifs of secondary >structure, do chainpacking studies down to the energeticly meaningful >manipulation of single atoms is SCULPT from Interactive Simulations. You can >download the program ( in a timebombed demoversion) from >http://www.intsim.com/~isigen. It's for free. There are also some meaningful >demostructures from actual scientific research work which can give you some >ideas of how to possibly approach your problem. > >This Demoversion runs on an SGI. There is now a first Versiobn for the >Powermacintosh available - with astounding speed! A PC version is coming >later this year. > >Hope this helps at least a little bit in your complicated problem. > >Almost forgot: There is a simple solution : just crystallize it and do the >structure :-) > >Cheers >Klaus > Klaus J.W. May e-mail: kmay@trans.net May & Partner Phone/Fax: xx49-(89) 333 569 SciTech Consult Mobile national: 0171-80 80 900 Mandlstr. 15 international: xx49-1712-80 80 900 D - 80802 Munich GERMANY