From ccl@www.ccl.net Tue Oct 8 11:54:03 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.0/950822.1) id LAA08327; Tue, 8 Oct 1996 11:00:39 -0400 (EDT) Received: from euch4e.chem.emory.edu for qiang@euch4e.chem.emory.edu by bedrock.ccl.net (8.8.0/950822.1) id LAA19903; Tue, 8 Oct 1996 11:00:39 -0400 (EDT) From: Received: from localhost by euch4e.chem.emory.edu (AIX 3.2/UCB 5.64/4.03) id AA21046; Tue, 8 Oct 1996 11:00:38 -0400 Date: Tue, 8 Oct 1996 11:00:38 -0400 (EDT) To: CCLink Subject: Re: CCL:Virial theorem... In-Reply-To: Message-Id: On Thu, 3 Oct 1996 qiang@euch4e.chem.emory.edu wrote: Sort of answer the question myself. It seems that virial's theorem doesn't hold at all for ECPs, but more or or less O.K. for non-ECP calculations. That's why I only found those huge -V/T value in pure metal cluster case, but more or less O.K. for complexes involving both metals (treated with ECP) and "standard" atoms (non-ECP). For cases with pure "standard" atoms, -V/T are always even closer to 2. > > Hi, dear CCL members: > > I've noticed that in some cases, the -V/T given in the output of > Gaussian94 is way off the correct value 2. I do know that in the usual ab > initio theory, virial theorem doesn't hold exactly (even though quite many > people are working along this line..), so a value close to 2 is good > enough. But in some of my calculations, I've got values around 4!! What > does this mean? Does this mean my calculation is not correct? I do notice > that in those cases, there are close lying states, I wonder how is this > related to my huge -V/T value. > > Any suggestions? Tons of thanks. > > ______________________________________________________________ > > Qiang Cui > Dept. of Chem. Emory Univ. 508 Webster Dr. Apt.#2 > Atlanta, GA 30322. Decatur, GA 30033. > (404)-727-2381 (404)-636-6149 > > http://tswww.cc.emory.edu/~qcui > ______________________________________________________________ > > > > > --- > 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 > --- > > ______________________________________________________________ Qiang Cui Dept. of Chem. Emory Univ. 508 Webster Dr. Apt.#2 Atlanta, GA 30322. Decatur, GA 30033. (404)-727-2381 (404)-636-6149 http://tswww.cc.emory.edu/~qcui ______________________________________________________________ From ccl@www.ccl.net Tue Oct 8 14:54:06 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.0/950822.1) id NAA10149; Tue, 8 Oct 1996 13:58:47 -0400 (EDT) Received: from saturn.kent.edu for raeker@saturn.kent.edu by bedrock.ccl.net (8.8.0/950822.1) id NAA24791; Tue, 8 Oct 1996 13:58:45 -0400 (EDT) Received: by saturn.kent.edu (AIX 4.1/UCB 5.64/4.03) id AA13838; Tue, 8 Oct 1996 13:50:03 -0400 Date: Tue, 8 Oct 1996 13:50:02 -0400 (EDT) From: "Todd J. Raeker" To: CCL Subject: CCL: Aniline Compounds Message-Id: Hello all, I am trying to find references reporting structures of aniline based on ab initio calculations and experiment. I did a search on a database I have access to but came up with nil. I can't believe this compound has been left alone. Anybody have references handy? Regards. Todd Dr. Todd J. Raeker Department of Chemistry Theoretical Chemistry Group Kent State University raeker@saturn.kent.edu Kent, OH 44242-0001 http://www.saturn.kent.edu/Raeker Phone (216)-672-2986 From ccl@www.ccl.net Wed Oct 9 10:13:47 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.0/950822.1) id JAA04082; Wed, 9 Oct 1996 09:53:42 -0400 (EDT) Received: from www.hyper.com for polowin@hyper.hyper.com by bedrock.ccl.net (8.8.0/950822.1) id JAA02847; Wed, 9 Oct 1996 09:53:35 -0400 (EDT) Received: from hyper.hyper.com (hyper.hyper.com [206.51.24.9]) by www.hyper.com (8.6.12/8.6.12) with SMTP id JAA11518 for <@www.hyper.com:chemistry@ccl.net>; Wed, 9 Oct 1996 09:54:25 -0400 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:chemistry@ccl.net id AA15668; Wed, 9 Oct 96 09:54:23 -0400 Date: Wed, 9 Oct 96 09:54:23 -0400 From: polowin@hyper.hyper.com (Joel Polowin) Message-Id: <9610091354.AA15668@hyper.hyper.com> To: chemistry@ccl.net (Computational Chemistry) Subject: Re: Gaussian cube visualization The CUBE data from a Gaussian calculation can be imported to HyperChem for SGI and displayed as 3D isosurfaces; the HyperChem package includes the necessary utility. A 30-day free demo license for HyperChem for SGI is available. The SGI demo is available for downloading by ftp from www.ccl.net, in the directory /pub/chemistry/software/SGI/HyperChem-demo . Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com WWW: http://www.hyper.com/ From ccl@www.ccl.net Wed Oct 9 10:13:53 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.0/950822.1) id JAA03977; Wed, 9 Oct 1996 09:30:50 -0400 (EDT) Received: from kodakr.kodak.com for lrbu00@xd88.kodak.com by bedrock.ccl.net (8.8.0/950822.1) id JAA02166; Wed, 9 Oct 1996 09:30:45 -0400 (EDT) From: Received: from euler.kodak.com by kodakr.kodak.com with SMTP id AA00436 (5.67b/IDA-1.5 for <@kodakr.kodak.com:chemistry@ccl.net>); Wed, 9 Oct 1996 09:30:00 -0400 Received: from xd88.kodak.com by euler.kodak.com via SMTP (940816.SGI.8.6.9/940406.SGI) id JAA01601; Wed, 9 Oct 1996 09:30:14 -0400 Received: by xd88.kodak.com (AIX 3.2/UCB 5.64/4.03) id AA18610; Wed, 9 Oct 1996 09:30:14 -0400 Date: Wed, 9 Oct 1996 09:30:14 -0400 Message-Id: <9610090930.ZM15024@xd88.kodak.com> X-Mailer: Z-Mail (3.0.0 15dec93) To: chemistry@ccl.net Cc: mckelvey@kodakr.kodak.com Netters: Two questions: 1) Does anyone know of a reference to Hartree-Fock calculations for atoms and the various types of ions that can be generated for the respective atoms? I would like to compare IP's and EA's from this approach to those found in Charlotte Moores' tables. 2) A subtle point I think I do not understand... but I think the answer is no. If one has a converged ROHF open-shell energy, wave function, density, etc, can one use a gradient code for UHF to get accurate gradients? Again I think not.. but I would appreciate any comments. Thanks! John -- John M. McKelvey email: mckelvey@Kodak.COM Computational Science Laboratory phone: (716) 477-3335 2nd Floor, Bldg 83, RL Eastman Kodak Company Rochester, NY 14650-2216 -- From ccl@www.ccl.net Wed Oct 9 12:13:46 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.0/950822.1) id LAA05346; Wed, 9 Oct 1996 11:58:46 -0400 (EDT) Received: from scripps.edu for rickr@scripps.edu by bedrock.ccl.net (8.8.0/950822.1) id LAA06235; Wed, 9 Oct 1996 11:58:43 -0400 (EDT) Received: from aries.scripps.edu by scripps.edu (5.61/1.34) id AA22504; Wed, 9 Oct 96 08:58:39 -0700 Received: by aries.Scripps.EDU (4.1/SMI-4.1) id AA15250; Wed, 9 Oct 96 08:58:31 PDT Date: Wed, 9 Oct 96 08:58:31 PDT From: rickr@scripps.edu (Rick Ross) Message-Id: <9610091558.AA15250@aries.Scripps.EDU> To: chemistry@ccl.net Subject: Industrial Comp. Chem. Symp. Final Call for Papers - Deadline October 25, 1996 Industrial Applications of Computational Chemistry 4 Days of Oral Presentations, a Panel Discussion, and a Poster Session are Scheduled. 1997 Spring National American Chemical Society Meeting Computers in Chemistry Division April 13-18, 1997 San Francisco, California Papers sought in all areas including applications such as catalysis, chemicals, coatings, engineering and/or theoretical chemical aspects of process design and modeling, glass, lubricants, petroleum, polymers, and other materials-orientated areas. Please send abstract on official ACS form to: Dr. Anne M. Chaka, The Lubrizol Corporation, 29400 Lakeland Boulevard, Wickliffe, OH 44092-2298; email: chaka@lubrizol.com. or Dr. Richard B. Ross, PPG Industries, P.O. Box 9, Allison Park, PA 15101; Voice: 412-492-5359; email: rbross@ppg.com. Abstracts due on official ACS forms no later than OCTOBER 25, 1996. From ccl@www.ccl.net Wed Oct 9 12:13:54 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.0/950822.1) id MAA05513; Wed, 9 Oct 1996 12:11:35 -0400 (EDT) Received: from gatekeeper.eastman.com for bewilson@eastman.com by bedrock.ccl.net (8.8.0/950822.1) id MAA06538; Wed, 9 Oct 1996 12:11:32 -0400 (EDT) Received: by gatekeeper.eastman.com; id MAA07124; Wed, 9 Oct 1996 12:12:01 -0400 Received: from emngw1.eastman.com(164.89.254.2) by gatekeeper.eastman.com via smap (g3.0.1) id xma007105; Wed, 9 Oct 96 12:11:35 -0400 Received: from ntb150.kpt.emn.com by eastman.com with SMTP id AA41894 (5.67b/IDA-1.5 for ); Wed, 9 Oct 1996 11:48:15 -0400 Received: by ntb150.kpt.emn.com with SMTP (Microsoft Exchange Server Internet Mail Connector Version 4.0.993.5) id <01BBB5D7.7CCCC010@ntb150.kpt.emn.com>; Wed, 9 Oct 1996 11:46:19 -0400 Message-Id: From: "Wilson, Bruce" To: "'chemistry@ccl.net'" Subject: Summary, unusual diffusion results in graphite Date: Wed, 9 Oct 1996 11:46:18 -0400 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.993.5 I note that I never did send in the summary of the responses to my questions on high temperature dynamics and diffusion in graphite. The question dealt with why we were getting gasses with permeabilities through graphite and asbestos that were in inverse order of size (largest molecules permeating most rapidly). I had thought there was a chemical effect. As it turns out, Bruce Luxon (bruce@nmr.utmb.edu), from the University of Texas provided the critical clue. Think "size exclusion chromatography". The smaller molecules are coming out more slowly because they are small enough to explore all of the microcracks and shafts in the graphitic and asbestos structures. In essence, they have a considerably higher pathlength to traverse than the larger molecules. ======================================= Bruce E. Wilson Eastman Chemical Company; Kingsport, TN (bewilson@eastman.com) http://www.eastman.com Voice: (423) 229-8886 FAX (423) 229-6114 The most difficult question for a theoretician to answer is "Who cares?" From ccl@www.ccl.net Wed Oct 9 18:13:53 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.0/950822.1) id SAA11381; Wed, 9 Oct 1996 18:13:10 -0400 (EDT) Received: from bioc1.msi.com for dgregory@msi.com by bedrock.ccl.net (8.8.0/950822.1) id SAA15618; Wed, 9 Oct 1996 18:13:01 -0400 (EDT) Received: from biff.msi.com by bioc1.msi.com (5.64/0.0) id AA08388; Wed, 9 Oct 96 15:12:32 -0700 Received: from [146.202.16.11] by biff.biosym.com (4.1/SMI-4.1) id AA13192; Wed, 9 Oct 96 15:12:28 PDT X-Sender: dgregory@146.202.0.225 Message-Id: Date: Wed, 9 Oct 1996 15:13:52 -0700 To: chemistry@ccl.net (Comp. Chem. List) From: dgregory@msi.com (Don Gregory) Subject: Re:Questions about Cerius2, Quanta, InsightII On Oct.9, Jeffery Nauss wrote: "> ...whom should I call about Cerius2, Quanta, and InsightII? I have some >questions about the future of the programs and how our department should deal >with it. Part of the whole merger process, was to spend quite a lot of time reviewing the technology overlap, and analyzing the capabilites of all the packages/modules, etc so as to determine the best way to go forward, not only to simplify our lives, but also to ensure that our customers were not left in the cold with respect to the scientific tools they were finding successful. Our sales force can relate the results of those analyses, and so I'd contact them with questions. If anyone would like any additional detail, or technical discussion on some of those analyses, they could contact the relevant product manager e.g. myself. In general, finding out who the right sales person is, or who the appropriate prod.mgr. is, can be done by reviewing our web pages. Hope this helps! Don Gregory Dr. Don Gregory (dgregory@msi.com) Molecular Simulations Inc. 9685 Scranton Rd. San Diego, CA 92121 (619) 546-5331 http://www.msi.com From ccl@www.ccl.net Thu Oct 10 06:13:50 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.0/950822.1) id FAA13526; Thu, 10 Oct 1996 05:30:04 -0400 (EDT) Received: from ra.abo.fi for arilahti@ra.abo.fi by bedrock.ccl.net (8.8.0/950822.1) id FAA19320; Thu, 10 Oct 1996 05:30:02 -0400 (EDT) Received: from kirke.abo.fi (arilahti@kirke.abo.fi [130.232.80.238]) by ra.abo.fi (8.7.3/8.7.3) with ESMTP id MAA28003 for ; Thu, 10 Oct 1996 12:30:00 +0300 (EET DST) From: Ari Lahti IFK Received: (arilahti@localhost) by kirke.abo.fi (8.6.10/8.6.9) id MAA29330 for chemistry@ccl.net; Thu, 10 Oct 1996 12:29:58 +0300 Message-Id: <199610100929.MAA29330@kirke.abo.fi> Subject: Temperature problem with CHARMm restart To: chemistry@ccl.net Date: Thu, 10 Oct 1996 12:29:56 +0300 (EET DST) X-Mailer: ELM [version 2.4 PL23] Dear CCLers, I'm trying to run a MD simulation on a small bio-organic molecule using CHARMm, version 23.1. I have a problem in keeping constant the temperature after a restart of the run. The temperature I want to use is 310 K, and my heating and equilibration phases have durations of 500 and 10 000 cycles (1 fs/cycle), respectively. At the end of the equilibration I have a temperature of 312 degrees. After that, everything works fine during the actual simulation run, unless I instead of a continuous run stop and restart the run again after the equilibration. The restarted run starts at 312 degrees but immediately thereafter the temperature goes down to 292 degrees. The temperature keeps at this low level all the way thereafter. I don't see what makes the temperature go down in the restarted run since I'm using the same parameters in both running methods. The right starting temperature at the beginning of the restarted run should guarantee that I'm using the right .RST file. Can anybody explain to me what the reason for this kind of behaviour might be? regards --ari ----------------------------------------------------------------------------- * Ari Lahti, M.D., M.Sc. tel.: +358-2-2654951 * * Dept. of Phys. Chem. fax: +358-2-2654706 * * Abo Akademi University e-mail: arilahti@abo.fi * * Porthansg. 3-5 * * FIN - 20500 Abo * * Finland * ----------------------------------------------------------------------------- From SZILAGYI@ps1515.chemie.uni-marburg.de Thu Oct 10 11:13:56 1996 Received: from Mailer.Uni-Marburg.DE for SZILAGYI@ps1515.chemie.uni-marburg.de by www.ccl.net (8.8.0/950822.1) id KAA14678; Thu, 10 Oct 1996 10:59:39 -0400 (EDT) Received: from ps1515.Chemie.Uni-Marburg.DE by Mailer.Uni-Marburg.DE (AIX 3.2/UCB 5.64/20.07.94) id AA70204; Thu, 10 Oct 1996 16:59:27 +0200 Received: from NWS_CHEMIE/MAILQ by ps1515.chemie.uni-marburg.de (Mercury 1.20); 10 Oct 96 17:01:33 GMT+2 Received: from MAILQ by NWS_CHEMIE (Mercury 1.20); 10 Oct 96 17:01:16 GMT+2 From: "Robert K. Szilagyi" To: chemistry@www.ccl.net Date: Thu, 10 Oct 1996 17:01:09 MDT Subject: G94 Makefile for Irix 4.0.5 Reply-To: szilagyi@mm2.vein.hu Cc: szilagyi@mm2.vein.hu Priority: normal X-Mailer: Pegasus Mail for Windows (v2.01) Message-Id: <2BD8E8F7B50@ps1515.chemie.uni-marburg.de> Dear Members, I am looking for a contact with people, who has any practice (and success ;-) on compilation of the G94 (Rev.C) on a Indigo R3000 IRIX4.0.5 platform. What I can do not understand at all, that the compilation stops without any error message and I do not know really what is the problem. I have tried the Gaussian Inc., but unfortunately, they do not support this platform any longer. Please respond me directly and If there will be something remarkable I will summarize for the net! Thanks in advance, Rob From ccl@www.ccl.net Thu Oct 10 13:14:01 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.0/950822.1) id NAA15771; Thu, 10 Oct 1996 13:12:53 -0400 (EDT) Received: from cliff.acs.oakland.edu for bbesler@ouchem.chem.oakland.edu by bedrock.ccl.net (8.8.0/950822.1) id NAA25902; Thu, 10 Oct 1996 13:12:47 -0400 (EDT) Received: from ouchem.chem.oakland.edu (ouchem.chem.oakland.edu [141.210.108.5]) by cliff.acs.oakland.edu (8.7.6/8.7.3) with SMTP id NAA28123 for ; Thu, 10 Oct 1996 13:14:32 -0400 (EDT) Received: by ouchem.chem.oakland.edu; id AA16317; Thu, 10 Oct 1996 13:13:39 -0400 From: "Brent H. Besler" Message-Id: <9610101713.AA16317@ouchem.chem.oakland.edu> Subject: Mysterious Problem with G94 on SGI/R10000K To: chemistry@ccl.net Date: Thu, 10 Oct 1996 13:13:39 -0500 (EDT) X-Mailer: ELM [version 2.4 PL21] I just installed G94 rev d4 on our SGI R10K. I am trying to run an unrestricted MP2 optimization. The calculation is mysteriously core dumping in l906 before it prints the MP2 energy. It gives no error messages. Has anyone seen this before? I have a new system from a week ago, because of the defective R10000 chip problem. From gadre@unipune.ernet.in Thu Oct 10 19:13:57 1996 Received: from sangam.ncst.ernet.in for gadre@unipune.ernet.in by www.ccl.net (8.8.0/950822.1) id SAA20682; Thu, 10 Oct 1996 18:27:48 -0400 (EDT) Received: from mail-relay-PUNE (mail-relay-pune.ernet.in [202.41.82.46]) by sangam.ncst.ernet.in (8.7.5) with SMTP id XAA13188 for ; Thu, 10 Oct 1996 23:52:45 +0530 (GMT+05:30) Received: from unipune.ernet.in by mail-relay-PUNE (5.65v3.2/SMI-4.1) id AA06995; Thu, 10 Oct 1996 18:42:36 +0500 Received: by unipune.ernet.in (5.0/SMI-SVR4.1.0) id AA01028; Thu, 10 Oct 1996 18:24:59 +0500 Date: Thu, 10 Oct 1996 18:24:59 +0500 From: gadre@unipune.ernet.in (Faculty) Message-Id: <9610102324.AA01028@unipune.ernet.in> To: CHEMISTRY@www.ccl.net Subject: XII ICCCRE Announcement Cc: gadre@unipune.ernet.in Status: RO ICCCRE XII First Announcement (MARK YOUR CALENDARS) ******** JANUARY 1998 *********** The Twelfth International Conference on Computers in Chemical Research and Education (ICCCRE XII) will be held at the University of Poona in Pune, India, in the week of 5-10 January 1998. Pune is one of the premier centers of learning in India, located about 100 miles south of Mumbai (Bombay). The purpose of the ICCCRE to present a sweeping and state-of-the-art description and critical examination of the applications of computers in chemistry presented by outstanding experts drawn from all over the world. The program will be organized such that all interested parties can experience a broad range of topics. There will be ample opportunities for small group and one-on-one discussions. In particular, it is our endeavour that the program will especially cater to the needs of junior faculty, researchers, and students who are just statring out in the field. In addition, those based in other disciplines, whose work overlaps with computers applied in chemistry, will be exposed to authoritative treatments of computers in chemistry and related disciplines. Tentatively, the technical program will focus on the following topics : (1) Computers in Chemical Education (2) Electronic Journals, Publishing and Conferencing (3) Artificial Intelligence, Chemometrics, Neural Networks and their Chemical Application. (4) Molecular Modeling, Quantitative Structure-Activity Relationship(QSAR). (5) Semi-Empirical and ab initio Quantum Chemistry, Density Functional Methods. (6) New Algorithms and Techniques in Computational Chemistry Under consideration is the possibility of pre-conference sharing of invited/contributed papers via electronic conferencing (a new feature of the ICCCRE). Given the rich and varied history and cultural attractions of India, the organizers hope to arrange pre-and/or post-conference excursions of varying duration. Programmatic suggestions and nominations for speakers are encouraged and are indeed very welcome. Please send your comments and/or let us know whether you would like to have your name and address added to the distribution list for further information via nay of the following channels : (1) Official Mailing Address : ICCCRE XII c/o Professor Shridhar R. Gadre Department of Chemistry University of Pune Pune - 411 007. INDIA e-mail : gadre@unipune.ernet.in phone : 91-212-351728 (2) World Wide Web Site (with form facility) http :// stu.Beloit. edu/chemistry/ICCCRE (3) Facilitators working with Professor S.R. Gadre : Professor Peter Lykos Professor Rama Viswanathan Illinois Inst. of Tech Beloit College Chicago, IL 60616. U.S.A. Beloit, WI 53511. U.S.A. 1-312-567 3430 1-608-363-2273 lykos@charlie.cns.iit.edu ramav@beloit.edu PLEASE HELP US TO PUBLICIZE ICCCRE XII BY FORWARDING AND/OR POSTING THIS ANNOUNCEMENT ON BULLETIN BOARDS, L-SERVS, WWW SITES. NEWSLETTERS, SOCIETY PUBLICATIONS AND CALENDARS AND YOUR OWN DISTRIBUTION LISTS. THANK YOU FOR YOUR INTEREST, HELP, AND COOPERATION. Professor Shridhar R. Gadre Department of Chemistry University of Pune Pune, INDIA. From shaomeng@helix.nih.gov Fri Oct 11 10:14:17 1996 Received: from helix.nih.gov for shaomeng@helix.nih.gov by www.ccl.net (8.8.0/950822.1) id JAA25391; Fri, 11 Oct 1996 09:50:46 -0400 (EDT) Received: (from shaomeng@localhost) by helix.nih.gov (950413.SGI.8.6.12/8.6.12) id JAA17255; Fri, 11 Oct 1996 09:50:34 -0400 Date: Fri, 11 Oct 1996 09:50:34 -0400 From: Shaomeng Wang Message-Id: <199610111350.JAA17255@helix.nih.gov> To: CHEMISTRY@www.ccl.net Subject: Replies to my original post: Motif software or database? Cc: shaomeng@helix.nih.gov Dear CCL friends, On Oct. 2, 96, I posted a message on the CCL about Motif searching software or database. I have received a number of replies to my question. I like to thank each of you for your time and information. Here is the collection of all the replies. ****************************************************************************** If you have coordinates for a protein with an unknown motif, try using Dali (http://www.embl-heidelberg.de/dali/dali.html). That will give you the names of all proteins with similar folds (and their motifs will probably be reported in the literature). Hope this is what you're looking for... Jane ******************************************* Jane Caldwell Biophysics Program/Dept. Biochemistry 420 Henry Mall University of Wisconsin-Madison Madison, WI 53706 E-mail: jane@nmrfam.wisc.edu ******************************************* Hi, You can find a list of available software for chemistry at: http://laaksonen.csc.fi/docs/stuff.html I hope this helps. -- ************************************************* Istvan Enyedy The Catholic University of America Chemistry Department/ Malloney Hall Washington DC 20064 email istvan@bioorg.ee.cua.edu phone 202-319-5707 or 5349 fax 202-319-5381 ************************************************** I vaguely remember that Prof. Janet Thornton published a series paper on protein motif and developed some software for this. I believe Oxford Molecular Group markets her software under the name Idditis. Check their web site. Shaomeng Wang wrote: > > Dear CCL friends, > > Could any provide me the information on the software/database for > searching for known protein motifs? > > I appreciate very much your information. > > Shaomeng Wang, Ph.D. > Georgetown University Medical Center > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: shaomeng@helix.nih.gov > -- Original Sender From: Address: shaomeng@helix.nih.gov > 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 -- Willie Cui, Ph.D. voice: (201)512-0486 MicroSimulations fax: (201)512-0489 478 Green Mountain Road info@microsimulations.com Mahwah, NJ 07430 http://www.microsimulations.com The PDB has theoretical models which may be of help. Professor David Eisenberg's group at UCLA would definitely know: cascio@uclaue.mbi.ucla.edu is a staff there and may know. Tell him I sent ya. AHSystems Group "Your Work Just Got Easier!" Contact Person: John Parikh 5401 Lakeford Lane, Suite L-1, Bowie, MD 20720,=20 Phone (301) 352-0896, Fax (301) 352-0199, Web Site www2.ari.net/ahsystems,= E-Mail jparikh@ari.net Product Briefs: HSC Chemistry for Windows (version 2.03) HSC Chemistry for Windows is a chemical reaction and equilibrium software= package which utilizes an extensive thermochemical database of over 7,600= compounds. The program includes 7 different calculation options for= computing Gibbs free energies and equilibrium constants for reaction= equations, heat and material balances, equilibrium compositions, formula= weights, electrochemical cell equilibria, phase stability diagrams, and= Eh-pH (Pourbaix) diagrams. Kinetics Kinetics numerically integrates the rate equations for reversible multistep= chemical reactions to determine the concentrations of the chemical species= in the system as a function of time. The program provides an easy to use= interface which allows users to create complex reaction systems by = entering the reactions of interest and the associated rate constants. No= other input is required by the program. The program formulates the required= rate equations from the list of reactions. Graphical output of results can= =20 be obtained, and an output file suitable for use in a spreadsheet program is= generated TAPP A Windows or Macintosh materials property database with thermophysical= property data for over 17,000 compounds and a collection of 1500 phase= diagrams.=20 TEP(Thermal Equilibrium Program) TEP is an interactive chemical combustion analysis tool for assessing the= products of combustion under equilibrium conditions using the minimization= of the Gibbs free energy. The NASA Lewis chemical equilibrium computer= program is used as the underlying solver. HyperChem, ChemPlus, and HyperNMR An extremely powerful molecular modeling package, HyperChem makes= computational chemistry more accessible to researchers and educators. = HyperChem is an integrated and flexible molecular modeling package that= offers a comprehensive set of tools for studying and predicting molecular= structures and properties. The program includes a number of computational= options (geometry=20 optimization, molecular dynamics, etc.) utilizing several well known= molecular mechanics and semiempirical computational methods. ChemPlus adds 9 extensions to HyperChem, including molecular rendering,= conformational searching, RMS overlap of molecules, sequence editing,= crystal and sugar building, and QSAR property calculations HyperNMR calculates chemical shifts and coupling constants using quantum= mechanics and simulates the resulting NMR spectrum PCModel PCModel is an interactive molecular modeling program for the study of = organic and inorganic molecules on your personal computer or workstation. = The program contains the MMX force field for performing computations.= PCModel has many applications for organic chemists, biochemists and = educators. -over- MOPAC 6.0 Mopac is a general purpose semiempirical molecular orbital package for the= study of chemical structures and reactions. The program includes the MNDO,= AM1, PM3, and MINDO/3 Hamiltonians Kekul=E9 Kekul=E9 for Windows and Mac provides unique technology for scanning and = automatically interpreting chemical structures. The Windows version= includes a full feature molecular editor, making this the most complete= molecular structure input system available PROCEDE for Windows Procede is an easy to use process design programs which can be used to= creates engineering drawings and specification sheets. The program includes= a symbol library manager, allowing users to add custom symbols to= flowsheets. Custom equipment data can also be entered into specification= sheets. OPTIMATR OPTIMATR is a computer for calculating optical properties of materials. A= database of optical properties is included for use during the computations TFCalc TFCalc enables users to design and analyze optical thin film coatings. = TFCalc computes the reflectance, transmittance, absorptance, phase-change, = electric field, and color of multilayer coatings consisting of dielectric= and metallic materials All products and trademarks are protected under appropriate laws and all= rights are reserved.=20 Special Bundle Offers Special Offer Regular Price (Commercial/Academic) (Commercial/Academic) AHS's ChemSuites=20 HSC Chemistry / Kinetics / TAPP (BEST DEAL!) $ 1280 / $1090 $ 1685 / $ 1485 HSC Chemistry / Kinetics $ 795 / $ 695 $ 1190 / $ 1090 HSC Chemistry / TAPP $ 995 / $ 895 $ 1090 / $ 990 Kinetics / TAPP $ 695 / $ 595 $ 1090 / $ 890 HyperChem 4.5 for Windows $ 2395/1195 $ 2595/ $ 1295 HSC Chemistry for Windows (LOWEST $$$!) $ 580 / $ 580(2 user lic.) $ 595 /= $ 595 (2 user lic.) Kinetics for Windows $ 295 / $ 195 $ 595 / $ 495 TAPP (FREE upgrades for next 12 months) $ 450 / $ 395 $ 495 / $ 395 Cad Crystallography $ 250 / $ 195 $ 349 / $ 299=09 TEP $ 550 / $ 450 $ 795 / $ 695 Shipping and handling charges not included in the prices. AHSystems Group - 5401 Lakeford Lane, Suite L-1, Bowie, MD 20720 - Phone= 301.352.0896 - Fax 301.352.0199 --=====================_844374534==_ Content-Type: text/plain; charset="us-ascii" John Parikh Marketing Manager AHSystems Group 5401 Lakeford Lane, Suite L-1 Bowie, MD 20720 Phone 301.352.0896 Fax 301.352.0199 Web Site www2.ari.net/ahsystems --=====================_844374534==_-- * ******************************************************************************** From feblm@csd.uwm.edu Fri Oct 11 13:14:31 1996 Received: from batch1.csd.uwm.edu for feblm@csd.uwm.edu by www.ccl.net (8.8.0/950822.1) id NAA26753; Fri, 11 Oct 1996 13:13:06 -0400 (EDT) Received: from alpha1.csd.uwm.edu (feblm@alpha1.csd.uwm.edu [129.89.169.1]) by batch1.csd.uwm.edu (8.7.6/8.6.8) with ESMTP id MAA26079 for ; Fri, 11 Oct 1996 12:13:07 -0500 (CDT) Received: (feblm@localhost) by alpha1.csd.uwm.edu (8.7.6/8.6.8) id MAA20683; Fri, 11 Oct 1996 12:13:03 -0500 (CDT) Date: Fri, 11 Oct 1996 12:13:03 -0500 (CDT) From: Patricia M Fulmer To: CHEMISTRY@www.ccl.net Cc: feblm#alpha1.csd.uwm.edu@alpha1.csd.uwm.edu Subject: Summary: Partial Charges on FAD with MOPAC Message-ID: MIME-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="0-677359431-845053983=:13061" This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. 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Fri, 11 Oct 1996 15:08:22 -0500 (CDT) Date: Fri, 11 Oct 1996 15:08:22 -0500 (CDT) From: Patricia M Fulmer Message-Id: <199610112008.PAA30469@alpha1.csd.uwm.edu> To: CHEMISTRY@www.ccl.net Subject: Summary: Partial Charges on FAD with MOPAC Cc: feblm@batch1.csd.uwm.edu With appologies for the previous post.... Dear Friends, On Sep. 23, 1996, I posted a message to you regarding calculation of partial charges on FAD using MOPAC. I have received a number of replies to my question. I would like to thank each of you for your time and information. Here is my original question together with a collection your replies. Please forgive me if I have left anyone out. ****************************************************************************** Suppose I would like a quick estimate of the partial charges on flavin adenine dinucleotide (FAD) using MOPAC. What keywords would you recomend? This poor molecule disociates with words like PM3 PULAY MMOK T=7200 XYZ Will post replys to the list. Thanks in advance. ****************************************************************************** Hi, I saw your posting about FAD. I have done some work on flavins and simply used MMOK PM3 XYZ or MMOK PM3 GEO-OK . Paul Heelis. p.s why the interest in FAD. I am a flavin man so I was just curious. Dr. P.Heelis Faculty of Science and Innovation North East Wales Institute Mold Rd Wrexham Ll11 2AW UK "Paul Heelis, Research" ****************************************************************************** Hi! Add EF HESS=1 or EF HESS=3 These will use an explicit start hessian and thus stop (hopefully) the dissociation (that is - if it is a optimiser problem). Otherwise, free out the degrees that break up the molecule , optimise and then free them and optimise. Cheers Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@bath.ac.uk | |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| |School of Chemistry |+144 1225 8262826 ext 5137 | |University of Bath | | |Bath, Avon, U.K. |Field: QM/MM modeling | ------------------------------------------------------------------- A J Turner ****************************************************************************** Hi, Firstly it looks like you've forgotten a keyword to tell MOPAC about the charge state of the molecule in question. If it's a dinucleotide (2 phosphates ?) then you should use the keyword CHARGE=-2. In the absence of this MOPAC will try to treat the system as an open shell species for which it will have severe convergence problems (hence the PULAY I guess). It will probably also be horribly slow due to the need to treat electrons in SOMOs with the half-electron approximation. For charges I'd use AM1 MEP-derived charges (keywords AM1 and ESP). Also, you should probably use the EF keyword to employ the eigenvector method of optimisation. Additionally, you may or may not wish to include the keyword PRECISE to increase the accuracy (and CPU) of your calculation. If the calculation finishes with a rather high gradient say >10.0 then you may also wish to include the keyword GNORM=value (e.g. 1.0) to try and force the calculation to a better minimum. Generally, I find that below a gradient of say 5.0 a lot of systems will change only slightly in geometry and the resultant charges. Hope this has been of assistance. William -- Dr. William A. Wylie | Senior Scientist | Computational Chemistry Dept. | Email: ww@proteus.co.uk Proteus Molecular Design Ltd. | Phone: +44 1625 500555 Lyme Green Business Park | Fax : +44 1625 500666 Macclesfield | Cheshire | SK11 0JL, United Kingdom | William Wylie ****************************************************************************** Dear Patricia Fulmer, I have just done an optimization of FAD using the keywords:- T=36000 XYZ MMOK AM1 NOINTER It took 43 minutes and 9.756 seconds on an SGI 4400 processor (200MHz) The starting structure was got from a Brookhaven file (1fnb) (mainly because I was too lazy to built it from scratch). This structure needed to have hydrogens added. At this stage I ran the structure through a molecular mechanics package to ensure that there were no bad contacts. In my experience with MOPAC, if there are bad contact, either the program will not run (unless you put GEO-OK as a keyword), or the structure will undergo a rearrangement or dissociate. The precaution of doing molecular mechanics is well worth while. I must add that the structure I used was not in a zwitterion form (i.e. there were hydrogens on the phosphate groups). It would probably be netter to do the zwitterion form. In any case if all you want is atom charges then the keyword 1SCF would probably do, and would give you the charges in a much shorter time. I would imagine that the option PM3 would work in a similar time. Yours sincerely, Peter Bladon. "P.Bladon" ****************************************************************************** You mentioned that the molecules dissociates. Perhaps you don't want to optimize the structure using MOPAC. If you can obtain the crystal structure from the Cambridge Crystallographic database, optimization of the structure should not be necessary. One simply performs the MOPAC calculation for the fixed structure which you provide. If you don't have access to the crystal structure, try generating it with molecular mechanics. The Klotho Web site is one place that will probably have a .pdb structure. You may need Babel to convert the format to one that your version of MOPAC can use. Refer to my Web page, http://pages.pomona.edu/~wsteinmetz/moldata.html for links to sources of data. Data for small molecules is found on the organic chemistry page. Wayne Steinmetz ****************************************************************************** My "default" for something like this is AM1 NOMM CHARGES= FAD should have some charges on it, as it is usually modeled. If you have protonated everything, then you won't need these. If you are doing a geometry optimization, I recommend EF. You may want to better specify termination criteria (GNORM= , etc.), and a few others (DDMIN= 0.0, LET if you ar using MOPAC 93). I do not recommend using cartesian coordinates. Depending on the environment of your FAD, you may want to look at charging in a dielectric medium. Try AMSOL for an aqeous wavefunction. . .it may have parameters for other solvents as well. MOPAC has the COSMO model, where you can specify the dielectric constant, but I don't have experience with this. Be very careful of the charging on the phosphorus. Stewart (or maybe Dewar or Holder) have warned about some peculiarities of AM1 with P. sb Steve.Bowlus@sandoz.com ****************************************************************************** Dear Patricia, If you have a good starting geometry (e.g. from crystal structures, or obtained with molecular mechanics computations) the Mopac keyword 1scf might be what you look for. It will give you the properties, such as charges, of the specified geometry without further optimizations. Hope this helps, Best regards, Han Zuilhof ****************************************************************************** ** Dr. Han Zuilhof ** e-mail: ZUILHOF@chem.chem.rochester.edu ** ** Department of Chemistry ** ** ** University of Rochester ** ** ** Rochester, NY, 14627 ** Fax: (716) 473-6889 ** ** USA ** Voice: (716) 275-2219 ** ****************************************************************************** ** ** ** "Excite a photochemist!" ** ** ** ****************************************************************************** ** ** ** Future address: Dept. of Chemistry; Columbia University; New York, NY. ** ** (from ca. half October '96) ** ** ** ****************************************************************************** Han Zuilhof ****************************************************************************** Hi, Patricia, It's been a long time since I checked my mail so you may already have an answer, but have you tried using "1SCF" This only does not alter the geometry but it will give you charges, and info about where the electrons are etc.. Of course you nedd to use a half way decent geometry for this to give reasonable results. Hope this helps Iain ________________________________________________________ Iain McVey Graduate Student Department of Chemistry Kent State University Kent, Ohio, U.S.A. imcvey@scorpio.kent.edu (330) 672 3731 Iain McVey ******************************************************************************