From chemistry-request@server.ccl.net Fri May 7 03:44:06 1999 Received: from kimia.um.edu.my ([202.185.71.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id DAA27085 for ; Fri, 7 May 1999 03:44:01 -0400 Received: by kimia.kimia.um.edu.my (5.x/SMI-SVR4) id AA07012; Fri, 7 May 1999 15:35:20 +0800 Date: Fri, 7 May 1999 15:35:19 +0800 (MYT) From: "Dr. Ibrahim Noorbatcha" To: CHEMISTRY@ccl.net Subject: transition state search Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear ALL, I think my query about TS search has been misunderstood. As a result, I got several replies regarding the availability of QM softwares. From the several requests that I have received for a summary of replies, I think there is enough interest in this topic. Hence let me rephrase my question. My original question is: (emphasis added) >Given a potential energy function of a molecular system, are there any ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >software available which can locate the transition state?. For example, there are several programs available which can be used to locate a minimum in a function. However, locating a transition state is not trivial. When I teach energy minimization techniques, I ask the students to minimize the functions using several techniques. I thought of including the transition state search techniques also in my lectures. For this purpose, it would be very nice if I can have a stand alone program which can be used to locate a transition state for a given potential energy function, if it exists. In response to my original question, Didier MATHIEU directed my attention to Introduction to Computational Chemistry book by Frank Jensen. I do not have access to this book. Does any body know whether this book gives the program also along with the algorithm?. Any body there willing to share their program and/or experience with various transition state search techniques. thanks, ibrahim ============================================================================ Dr. Ibrahim Ali Noorbatcha Email: ibrahim@kimia.um.edu.my Department of Chemistry Phone: 603-759-4260 Universiti Malaya Fax : 603-759-4193 50603 Kuala Lumpur Malaysia ============================================================================= From chemistry-request@server.ccl.net Fri May 7 04:53:57 1999 Received: from ck-sg.p.lodz.pl (ck-sg.p.lodz.pl [212.51.207.68]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA27784 for ; Fri, 7 May 1999 04:53:51 -0400 Received: from piotr.p.lodz.pl (pc-212-51-214-182.p.lodz.pl [212.51.214.182]) by ck-sg.p.lodz.pl (980427.SGI.8.8.8/970903.SGI.AUTOCF-1) via SMTP id KAA13276 for ; Fri, 7 May 1999 10:47:44 +0200 (MDT) Message-ID: <01fc01be9866$0efcfea0$b6d633d4@p.lodz.pl> From: "Paneth" To: Subject: PM3tm Date: Fri, 7 May 1999 10:46:11 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Folks! I'm trying to calculate a transition state containing Co using PM3tm. I've got two programs, which have this parametrization: Hyperchem 5.1 and PC Spartan Pro. The problem is I've got also two different results: 1. bond distances in the TS differ by about 0.1 A for the moving hydrogen 2. listed energies are completely different, e.g., -400 kcal/mol in Hyperchem vs. 1600 kcal/mol in Spartan (unfortunately it does not look like a printout mistake J for cal since the energetic differences between TS and reactants are also substantially different) Thus my question: could someone provide me with/ point me to a good model to test, which program gives correct results or another implementation of PM3tm? Thanks in advance, Piotr ****************************************************** Professor Piotr Paneth Department of Chemistry, Technical University Zeromskiego 116, 90-924 Lodz, Poland phone/fax: (+48 42) 631-3199 fax: (+48 42) 636-5008 From chemistry-request@server.ccl.net Thu May 6 05:49:05 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA12494 for ; Thu, 6 May 1999 05:49:04 -0400 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA03328 Thu, 6 May 1999 05:44:10 -0400 (EDT) Received: from rrzs2.rz.uni-regensburg.de (rrzs2.rz.uni-regensburg.de [132.199.1.2]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id FAA02261 for ; Thu, 6 May 1999 05:44:04 -0400 (EDT) Received: from rchs4.chemie.uni-regensburg.de (rchs4.chemie.uni-regensburg.de [132.199.48.4]) by rrzs2.rz.uni-regensburg.de (8.8.8/8.8.8) with SMTP id LAA19646 for ; Thu, 6 May 1999 11:43:47 +0200 (MET DST) Date: Thu, 6 May 1999 11:47:39 +0200 From: Herbert Homeier t4720 Message-Id: <9905060947.AA03752@rchs4.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: Q: Methods for transition states of radical cations Content-Transfer-Encoding: 7bit Mime-Version: 1.0 Reply-To: herbert.homeier@na-net.ornl.gov X-8Bit-Info: No 8bit-mail on this system X-Sun-Charset: ISO-8859-1 Dear CCL members, some colleagues are interested in calculations of radical cations containing about 10 C, some N and O and about 15 H with extended pi systems (distonic ions). They have the following questions that I would like to forward to the experts of such calculations in practice: A) What do you consider as state-of-the-art method(s) for calculating the energy of transitions states of such systems with an accuracy of about 5 kcal/mol? (Is this accuracy really realistic to expect?) B) Do you regard semiempirical methods as reliable for the calculation of the energy barriers of such systems? If yes, which ones? Also, pointers to literature on such issues would be appreciated. I will summarize the answers to CCL if there is sufficient interest. Thank you very much for your attention. Best regards Herbert Homeier -------------------------------------------------------------- Priv.-Doz. Dr. Herbert H. H. Homeier Institut für Physikalische und Theoretische Chemie Universität Regensburg, D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX: +49-941-943 4719/+49-941-943 2305 email: herbert.homeier@na-net.ornl.gov WWW: http://www.chemie.uni-regensburg.de/~hoh05008 From chemistry-request@server.ccl.net Thu May 6 06:42:50 1999 Received: from terra.pianeta.it (root@terra.pianeta.it [212.22.128.12]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA12893 for ; Thu, 6 May 1999 06:42:48 -0400 Received: from worgas.pianeta.it (i125.modena.pianeta.it [212.22.128.125]) by terra.pianeta.it (8.9.1/8.9.1) with SMTP id MAA17256 for ; Thu, 6 May 1999 12:37:45 +0200 Message-ID: <001d01be97ac$67df2940$5a0107c0@worgas.pianeta.it> From: "worgas" To: Subject: CHEMKIN Code Help Date: Thu, 6 May 1999 12:36:45 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0018_01BE97BD.1A6B3800" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Messaggio a più sezioni in formato MIME. ------=_NextPart_000_0018_01BE97BD.1A6B3800 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Dear CCL members, Does anybody have any experience with CHEMKIN code? I would appreciate your contacting me on this matter. I need of advises and any suggestions to use this software. Thanks a lot in advance Enrica Baraldi - PhD student Department of Engineering University of Modena, Italy worgas@worgas.it ------=_NextPart_000_0018_01BE97BD.1A6B3800 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear CCL members,

Does anybody have any experience with CHEMKIN code?

I would appreciate your contacting me on this matter. I need of = advises and=20 any suggestions to use this software.

Thanks a lot in advance

Enrica Baraldi - PhD student

Department of Engineering

University of Modena, Italy

worgas@worgas.it

 

 

------=_NextPart_000_0018_01BE97BD.1A6B3800-- From chemistry-request@server.ccl.net Thu May 6 12:28:02 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA18679 for ; Thu, 6 May 1999 12:28:02 -0400 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA04585 Thu, 6 May 1999 12:23:03 -0400 (EDT) Received: from europe.std.com (europe.std.com [199.172.62.20]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id MAA10124 for ; Thu, 6 May 1999 12:23:02 -0400 (EDT) Received: from world.std.com by europe.std.com (STD1.2/BZS-8-1.0) id MAA07805; Thu, 6 May 1999 12:23:03 -0400 (EDT) Received: by world.std.com (TheWorld/Spike-2.0) id AA05651; Thu, 6 May 1999 12:23:03 -0400 Date: Thu, 6 May 1999 12:23:03 -0400 From: jle@world.std.com (Joe M Leonard) Message-Id: <199905061623.AA05651@world.std.com> To: chemistry@ccl.net Subject: Question about PDB header dates - Y2K Folks, It seems that the PDB file header has dates in the form: DD-MMM-YY So, what should the date be next year - DD-MMM-00 or will the new custodians switch to DD-MMM-2000? Inquiring minds (who have to take care of I/O routines) want to know... Thanks in advance! Joe Leonard jle@world.std.com From chemistry-request@server.ccl.net Thu May 6 16:03:41 1999 Received: from tiger.jsums.edu (tiger.jsums.edu [143.132.85.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA21694 for ; Thu, 6 May 1999 16:03:40 -0400 Received: (from jerzy@localhost) by tiger.jsums.edu (980427.SGI.8.8.8/980728.SGI.AUTOCF) id OAA54672 for CHEMISTRY@ccl.net; Thu, 6 May 1999 14:53:46 -0500 (CDT) Date: Thu, 6 May 1999 14:53:46 -0500 (CDT) From: jerzy@tiger.jsums.edu (Jerzy Leszczynski) Message-Id: <199905061953.OAA54672@tiger.jsums.edu> To: CHEMISTRY@ccl.net Subject: 8th CCTCC Conference April 26, 1999 Dear Colleague: We are pleased to announce the eighth conference on Current Trends in Computational Chemistry. This symposium, organized by Jackson State University, will cover all areas of computational chemistry as well as quantum chemistry. The local host of the conference is the US Army Corps of Engineers Waterways Experiment Station (WES) in Vicksburg, Mississippi. The meeting will be held at the Holiday Inn of Vicksburg, Mississippi (40 miles west of Jackson) on November 5th and 6th, 1999. The format consists of a series of plenary lectures and poster presentations on Friday and Saturday covering applications as well as theory. In addition, a banquet is scheduled for Friday evening and a dinner and reception for Saturday evening. The 8th conference will also feature another talk given in the ancillary "Noble Lecture Series." This series was initiated during the 6th CCTCC by a remarkable presentation by Istvan Hargittai entitled "The Molecules Among Us: Conversations with Famous Chemists" and followed by a lecture "Past and Future of the Fullerene Story" delivered by Eiji Osawa during the 7th CCTCC. The lectures in this series are presented in a relaxed, after-dinner atmosphere by the noble speakers and are devoted to noble scientific events and people. As such, it is an exceptional lecture to the conference and, contrary to the regular talks, might not necessarily report any Current findings. This year the talk will be delivered by Michael Kasha, Florida State University. We are planning to publish extended abstracts (up to four pagers each) of all invited talks and poster presentations. Original scientific contributions will be published in a special issue of the Journal of Molecular Structure (TEOCHEM). Manuscripts for inclusion in the special issue should be submitted in triplicate upon arrival at the registration desk. Submitted papers will be subject to the journal's standard referee procedures. Sincerely, Jerzy Leszczynski Chairman of the Organizing Committee 8th CONFERENCE ON Current Trends In Computational Chemistry NOVEMBER 5 & 6, 1999, Vicksburg, Mississippi 1. NAME:________________________________________________________________________ 2. MAILING ADDRESS:_____________________________________________________________ ________________________________________________________________________________ TELEPNONE:_______________FAX:_______________E-MAIL:_______________________ 2. If you wish to present a poster, please indicate the title below. All abstracts are due by September 1, 1999 (up to 4 pagers in length, presenting author underlined, photo ready quality, in duplicate) to ensure publication in the Conference Materials. TITLE:__________________________________________________________________________ ________________________________________________________________________________ AUTHORS: _______________________________________________________________________ 3. Conference materials, banquet and reception fee, all meals from breakfast Friday through dinner Saturday, coffee, and refreshments are included per paid participant. MAKE CHECKS PAYABLE TO: Current Trends in Computational Chemistry. Registration fee before September 1, 1999 US$ 150.00 $_____ Registration fee thereafter 200.00 $_____ Registration fee at student discount 75.00 $_____ 4. HOUSING: the organizers will not make housing reservations. To reserve a room at the special conference rate of $50.00-$60.00 per room, contact the Holiday Inn of Vicksburg, 3330 Clay Street, Vicksburg, MS 39180, Tel: (601) 636-4551, fax: (601) 636-4552. Reservations should be arranged with the Holiday Inn prior to October 10, 1999. I do____do not____plan to stay at the conference hotel I do____do not____plan to submit a paper to the special issue of TEOCHEM ________________ Signature http://tiger.jsums.edu/~cctcc/conf_ homepage.html Department of Chemistry, Jackson State University, Jackson, MS 39217, USA Conference Chairman: Jerzy Leszczynski, Tel: 601-973-3482, Email: jerzy2.iris5.jsums.edu; Conference Secretary: Ms. Shonda R. Allen, Tel: 601-973-3723, Email: srallen@stallion.jsums.edu List of Invited Speakers Misako Aida Hiroshima University Isaac B. Bersuker The University of Texas at Austin Ernest Roy Davidson Indiana University Martin Field Institut de Biologie Structurale-Jean- Pierre Ebel William L. Jorgensen Yale University Michael Kasha Florida State University Morris Krauss Center for Advanced Research in Biotechnology Jan Labanowski Ohio Supercomputer Center Mark Olson USAMRIID, Frederick Mario Raimondi Universita' di Milano George Ch. Schatz Northwestern University Ajit J. Thakkar University of New Brunswick Harel Y. Weinstein Mount Sinai School of Medicine From chemistry-request@server.ccl.net Fri May 7 11:45:25 1999 Received: from chem.chem.rochester.edu (root@chem.chem.rochester.edu [128.151.176.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA32488 for ; Fri, 7 May 1999 11:45:24 -0400 Received: from markov.chem.rochester.edu (markov.chem.rochester.edu [128.151.176.16]) by chem.chem.rochester.edu (8.8.5/8.8.5) with SMTP id LAA11851; Fri, 7 May 1999 11:40:30 -0400 (EDT) Received: by markov.chem.rochester.edu (920330.SGI/920502.SGI.AUTO) for @chem.chem.rochester.edu:Chemistry@ccl.net id AA18250; Fri, 7 May 99 11:40:08 -0400 Date: Fri, 7 May 1999 11:40:02 -0400 (EDT) From: Sergei Tretiak To: Jian Wang Cc: Chemistry@ccl.net Subject: Re: CCL:news group In-Reply-To: <37325A9A.D0609113@indigo.ucdavis.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Jian, There may be several reasons for segmentation fault. Apart from some bugs in the code, first, try to compile your code with "-static" keyword (the syntax depends from your compiler) and see whether it helps. Next you could try to compile with "-check-bounds" keyword (again, look for the correct syntax for your compiler). Hopefully this will help before you will start hunting for the bugs. Sergei .-----------------------------------------------------------------------. |\ / \ | Sergei Tretiak | / \ /| |.\/...\|.......................................................|/...\/.| | Department of Chemistry | Voice: (716) 275-8289 | | University of Rochester | Fax: (716) 473-6889 | | P. O. Box 270216 | E-mail: serg@markov.chem.rochester.edu | | Rochester, NY 14627-0216 | serg@wigner.chem.rochester.edu | | Homepage: http://markov.chem.rochester.edu/serg/welcome.html | |_______________________________________________________________________| On Thu, 6 May 1999, Jian Wang wrote: > Hello, > > I have a Fortran code, it runs ok when the dimension of array is small, > but gives Segmentation fault when the array is large. Compile does not > show prblem though. > > Does anyone know a debug utility in Fortran, like gdb in C. > > > jwang > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Fri May 7 05:18:29 1999 Received: from kasei.materials.ox.ac.uk (kasei.materials.ox.ac.uk [163.1.64.46]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA28051 for ; Fri, 7 May 1999 05:18:28 -0400 Received: from localhost (hfield@localhost) by kasei.materials.ox.ac.uk (8.8.7/8.8.7) with ESMTP id KAA25418 for ; Fri, 7 May 1999 10:12:29 +0100 X-Authentication-Warning: kasei.materials.ox.ac.uk: hfield owned process doing -bs Date: Fri, 7 May 1999 10:12:28 +0100 (GMT) From: Andrew Horsfield X-Sender: hfield@kasei.materials.ox.ac.uk Reply-To: Andrew Horsfield To: Computational Chemistry List Subject: Beyond Born-Oppenheimer Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I am interested in studying non-radiative transitions in silicon, and have submitted a couple of postings to this list about non-adiabatic molecular dynamics. In the light of the responses I have received I am now fully persuaded of the need to have a very accurate description of the Born-Oppenheimer states in order to determine the small non-adiabatic correction. The most transparent way to proceed (I believe) would be to calculate the full wavefunction as a linear combination of Born-Oppenheimer states for the ground state and low lying excited states. A harmonic approximation for the ionic part of the wavefunction would be quite adequate. Non-radiative transitions could then be found by taking suitable matrix elements. Can it be done? Would this produce accurate wavefunctions? Are there standard procedures for doing this? Best regards, Andrew +----------------------------------------------------+ Andrew Horsfield e-mail: horsfield@fecit.co.uk FECIT, 2 Longwalk Road, Stockley Park, Uxbridge, Middlesex UB11 1AB, United Kingdom. phone: +44-(0)181-606-4653 FAX: +44-(0)181-606-4422 +----------------------------------------------------+ From chemistry-request@server.ccl.net Fri May 7 07:15:06 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA29006 for ; Fri, 7 May 1999 07:15:06 -0400 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA07776 Fri, 7 May 1999 07:09:55 -0400 (EDT) Received: from bacchus.pc1.uni-duesseldorf.de (jochen@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id HAA29246 for ; Fri, 7 May 1999 07:09:52 -0400 (EDT) Received: from [[UNIX: localhost]] ([[UNIX: localhost]]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) id NAA32643 for chemistry@ccl.net; Fri, 7 May 1999 13:09:43 +0200 From: Jochen Kuepper Organization: Heinrich-Heine-Universitaet To: CCL Subject: Fwd: FORTRAN (was: CCL:news group) Date: Fri, 7 May 1999 13:09:28 +0200 X-Mailer: KMail [version 1.0.21] Content-Type: text/plain MIME-Version: 1.0 Message-Id: <99050713094302.26174@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id HAA29007 On Fre, 07 Mai 1999 you wrote: >I have a Fortran code, it runs ok when the dimension of array is small, >but gives Segmentation fault when the array is large. Compile does not >show prblem though. Probably these are automatic variables ? Then you have to increase you stack size or to use a compiler flag to allocate automatic variables on the heap. For the first way you have to be sysadmin on many systems, the second way is not feasible with all compilers :-) Greetings, Jochen ----------------------------------------------------------------------- Jochen Küpper Heinrich-Heine-Universität Düsseldorf jochen@uni-duesseldorf.de Institut für Physikalische Chemie I Universitätsstr. 1, Geb 26.43 Raum 02.29 phone ++49-211-8113681 40225 Düsseldorf fax ++49-211-8115195 Germany http://www-public.rz.uni-duesseldorf.de/~jochen ----------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri May 7 09:15:03 1999 Received: from Bespin.worldnet.net (bespin.worldnet.net [195.3.3.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA30361 for ; Fri, 7 May 1999 09:15:02 -0400 Received: from a6y8p4 (wn16-229.paris.worldnet.fr [195.3.16.229]) by Bespin.worldnet.net (8.8.8/8.8.8) with SMTP id PAA29423 for ; Fri, 7 May 1999 15:07:08 +0200 (CEST) Message-ID: <002501be986c$ce487ea0$e51003c3@a6y8p4> From: "patrick urbaniak" To: Subject: Commercial Announcement: Cadcom/ProChemist Date: Fri, 7 May 1999 11:34:28 +0200 Dear Sir, Please note our web adress: http://home.worldnet.fr/cadcom/ Our company is providing a 3D molecular modeling = software(ProChemist),including Logp,Pka,Solubility.., calcs,Qsar,and chemometrics(neuronal network and >Genetic = Algorithms),running under Windows. We would appreciate to be referenced in your Web Site. Please feel free to contact us for further information =20 Best Regards P.Urbaniak(Cadcom) From chemistry-request@server.ccl.net Fri May 7 15:13:58 1999 Received: from smb.chem.niu.edu (smb.chem.niu.edu [131.156.9.3]) by server.ccl.net (8.8.7/8.8.7) with SMTP id PAA03078 for ; Fri, 7 May 1999 15:13:58 -0400 Received: from smb by smb.chem.niu.edu via SMTP (940816.SGI.8.6.9/940406.SGI) for id OAA28812; Fri, 7 May 1999 14:04:11 -0500 Sender: smb@smb.chem.niu.edu Message-ID: <3733392A.237C@smb.chem.niu.edu> Date: Fri, 07 May 1999 14:04:10 -0500 From: Steven Bachrach X-Mailer: Mozilla 3.01 (X11; I; IRIX 5.3 IP12) MIME-Version: 1.0 To: computational chemistry list Subject: Preannouncment ECCC6 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id PAA03079 Pre-Announcement The Sixth Electronic Computational Chemistry Conference will be held in November 1999. Continuing on the pathway set by the previous ECCC meetings, ECCC6 will be a completely electronic conference covering all aspects of computational chemistry. Registration will be free and we invite all interested parties to contribute an article and participate. The proceedings of ECCC6 will be published in the Internet Journal of Chemistry. ECCC6 will be organized by Herbert Homeier, Universität Regensburg, with assistance from the previous organizational team led by Steven Bachrach, Northern Illinois University. We hope to add some new features to ECCC6 and welcome any and all suggestions. Complete information on how to submit abstracts, registration and all other details will be coming in mid-summer. Herbert Homeier, Organizer ECCC6 Steven Bachrach, associate organizer, ECCC6 -- Priv.-Doz. Dr. Herbert H. H. Homeier Institut für Physikalische und Theoretische Chemie Universität Regensburg, Germany Phone: +49-941-943 4720 FAX: +49-941-943 4719/+49-941-943 2305 email: herbert.homeier@na-net.ornl.gov WWW: http://www.chemie.uni-regensburg.de/~hoh05008 Steven Bachrach Department of Chemistry and Biochemistry Northern Illinois University DeKalb, IL 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From chemistry-request@server.ccl.net Fri May 7 16:02:03 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA04022 for ; Fri, 7 May 1999 16:02:02 -0400 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA09891 Fri, 7 May 1999 15:56:48 -0400 (EDT) Received: from gateway.bioreason.com (bioreason.com [207.108.245.3]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id PAA15282 for ; Fri, 7 May 1999 15:56:45 -0400 (EDT) Received: from bioreason.com (val [192.168.1.51]) by gateway.bioreason.com (8.9.3/8.9.3) with ESMTP id NAA12539; Fri, 7 May 1999 13:48:48 -0600 Sender: dalke@bioreason.com Message-ID: <37334394.9978FD1C@bioreason.com> Date: Fri, 07 May 1999 13:48:36 -0600 From: Andrew Dalke Organization: Bioreason, Inc. X-Mailer: Mozilla 4.05C-SGI [en] (X11; U; IRIX64 6.5 IP30) MIME-Version: 1.0 To: Joe M Leonard CC: chemistry@ccl.net, pdb-l@rcsb.org Subject: Re: CCL:Question about PDB header dates - Y2K References: <199905061623.AA05651@world.std.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Joe M Leonard > Folks, > > It seems that the PDB file header has dates in the form: > > DD-MMM-YY > > So, what should the date be next year - DD-MMM-00 or will > the new custodians switch to DD-MMM-2000? Inquiring minds > (who have to take care of I/O routines) want to know... (I've cc'ed this reply to the PDB-L mailing list as well since that's the more appropriate venue.) I believe the proper treatment is to rollover to 00, since the date is a fixed format with two years for the year. 30-DEC-99 31-DEC-99 01-JAN-00 02-JAN-00 (rollover) In this case, you would have to know that the earliest PDB record is the obsolete "1B5C" from 10-AUG-72. This is conviently close to the unix/posix 0 date of Jan. 1, 1970 so you can map: 70-99 --> 1970-1999 00-69 --> 2000-2069 and after that hope that everyone has migrated to mmCIF or CML or some other more exensible file format. However, looking at the format definition, every card which uses a "Date" type (HEADER, OBSLTE, REVDAT, and SPRSDE) contains at least two unused characters afterwards, so there is the backwards compatible *possible* solution of using: DD-MMM-YYCC where the "CC" represent something like a century. There are two solutions here, the perl way, where the year written is the real year - 1900 (so 2000 is "100"), and the Javascript way, where the sequence of years is 98, 99, 2000, 2001. So the date could be represented as: 30-DEC-99 31-DEC-99 01-JAN-001 02-JAN-001 (the perl way) 30-DEC-99 31-DEC-99 01-JAN-0020 02-JAN-0020 (the javascript way) I've not heard the official PDB policy to this regard, but I'll bet they've decided to do the rollover solution. In any case, they'll have to change their format definition for "Date" listed at http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_85.html which currently says: | Date A 9 character string in the form dd-mmm-yy where DD is the | day of the month, zero-filled on the left (e.g., 04); MMM is | the common English 3-letter abbreviation of the month; and | YY is a year in the 20th century. Hopefully along with this fix they will address the format definition problems listed in the mailing list thread starting with: http://www.pdb.bnl.gov/hypermail/1074.html Andrew Dalke dalke@bioreason.com From chemistry-request@server.ccl.net Fri May 7 19:07:44 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA05876 for ; Fri, 7 May 1999 19:07:43 -0400 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA10429 Fri, 7 May 1999 19:02:27 -0400 (EDT) Received: from franc.ucdavis.edu (root@franc.ucdavis.edu [169.237.105.2]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id TAA24149 for ; Fri, 7 May 1999 19:02:27 -0400 (EDT) Received: from indigo.ucdavis.edu (indigo.ucdavis.edu [169.237.38.19]) by franc.ucdavis.edu (8.9.3/UCD3.13.10) with ESMTP id QAA21168 for ; Fri, 7 May 1999 16:02:22 -0700 (PDT) Received: from indigo.ucdavis.edu (kappa.ucdavis.edu [169.237.38.55]) by indigo.ucdavis.edu (8.8.8/UCD3.12.10) with ESMTP id QAA14696 for ; Fri, 7 May 1999 16:03:04 -0700 (PDT) Sender: jwang@indigo.ucdavis.edu Message-ID: <37337126.1326BA0A@indigo.ucdavis.edu> Date: Fri, 07 May 1999 16:03:03 -0700 From: Jian Wang X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX64 6.2 IP28) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:news group References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, Thanks for all expert advices regarding the segmentation fault posted yesterday. I suspected the segmentation fault comes from the array size, because it occurs when I increased the array size to around (220X659)=144980 under double precision (see the following output from the dbx). But If I test a simple code with an array of this size, it doesn't report error. My machine has still got a lot memory available (more than 2gb), so it is not possible the memory is run out on the machine. Some friend suggested it might be the limit on stack size which restrict the declaration of memory, which I think it is probable if no only the variables, but subroutine calls might also require stack. Can any expert give an detail as to how the stack, heap work in Fortran77? Jian ps: the test result: (dbx) r signal Segmentation fault at [current:69 ,0x120003d94] dimension Cmo1b(nocc-1,nbf),Cmo2b(nocc-1,nbf) (dbx) where > 0 current(NATOMS = 109, NOCC = 220, NBF = 659, NSHELL = 399, NP = 1073) ["current.for":69, 0x120003d94] 1 main() ["current.for":40, 0x1200030b8] 2 main() ["for_main.c":203, 0x1200029cc] From chemistry-request@server.ccl.net Fri May 7 21:44:09 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA07046 for ; Fri, 7 May 1999 21:44:08 -0400 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id VAA10688 Fri, 7 May 1999 21:38:52 -0400 (EDT) Received: from mail1.austin.rr.com ([24.93.35.128] (may be forged)) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id VAA25546 for ; Fri, 7 May 1999 21:38:50 -0400 (EDT) Received: from mjodalfr ([24.93.36.39]) by mail1.austin.rr.com with Microsoft SMTPSVC(5.5.1875.185.18); Fri, 7 May 1999 20:35:24 -0500 Message-ID: <005001be98f3$38f7ee80$0300a8c0@austin.rr.com> From: "Kenneth W. Egan" To: "Jian Wang" , References: <37337126.1326BA0A@indigo.ucdavis.edu> Subject: Re: CCL:news group Date: Fri, 7 May 1999 20:36:40 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 If you're running some derivative of unix......... use ulimit ulimit -s XXXXXX sets stack to XXXXXX KB's ulimit -d XXXXX sets data area to XXXXX KB's ulimit -m XXXXX ssets physical mem might try ulimit -s unlimited -d unlimited -m unlimited ----- Original Message ----- From: Jian Wang To: Sent: Friday, May 07, 1999 6:03 PM Subject: CCL:news group > Hello, > Thanks for all expert advices regarding the segmentation fault posted > yesterday. > I suspected the segmentation fault comes from the array size, because it > occurs when I increased the array size to around (220X659)=144980 under > double precision (see the following output from the dbx). > But If I test a simple code with an array of this size, it doesn't report > error. My machine has still got a lot memory available (more than 2gb), so > it is not possible the memory is run out on the machine. Some friend > suggested it might be the limit on stack size which restrict the > declaration of memory, which I think it is probable if no only the > variables, but subroutine calls might also require stack. > Can any expert give an detail as to how the stack, heap work in Fortran77? > > Jian > > ps: the test result: > > (dbx) r > signal Segmentation fault at [current:69 ,0x120003d94] dimension > Cmo1b(nocc-1,nbf),Cmo2b(nocc-1,nbf) > (dbx) where > > 0 current(NATOMS = 109, NOCC = 220, NBF = 659, NSHELL = 399, NP = 1073) > ["current.for":69, 0x120003d94] > 1 main() ["current.for":40, 0x1200030b8] > 2 main() ["for_main.c":203, 0x1200029cc] > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > >