From chemistry-request@ccl.net Wed Aug 5 10:29:01 1992 Date: Wed, 5 Aug 92 08:39:04 -0400 From: nobody@Kodak.COM To: "chemistry@ccl.net"@Kodak.COM Subject: Neural nets and DNA sequences. Status: R >From: NAME: Adi M. Treasurywala FUNC: Biophys. & Compu. Chem. TEL: (518)445-7042 To: "chemistry@ccl.net"@kodakr@mrgate@wpc Netters, I am interested in any information that anyone may have about the use of neural nets to deduce anything about sequences of DNA or RNA. It is an area that I have no experience in so any and all pointers would be most welcome. I am reasonably familiar with the applications of neural nets in protein sequence homologies etc. If there is sufficient interest I would be happy to summarize for the net. Thanks in advance, Adi T. PS: Please respond directly to me at the e-mail address shown below. Please do NOT reply to "NOBODY@kodak.com" (That's just my status... not my e-mail address) The correct address is adit@kodak.com. --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From MAALOUF@RISVAX.ROWLAND.ORG Wed Aug 5 10:37:51 1992 Date: Wed, 5 Aug 1992 10:36:57 -0400 (EDT) From: MAALOUF@RISVAX.ROWLAND.ORG Subject: PDB coordinate files To: CHEMISTRY-REQUEST@ccl.net Status: R Is there an FTP site or mail server for PDB coordinate files? From chemistry-request@ccl.net Wed Aug 5 11:31:55 1992 From: Matthew E. Harbowy Subject: mopac 6.0 To: CHEMISTRY@ccl.net (computational chemists) Date: Wed, 5 Aug 92 9:07:04 EDT Status: R Headaches and frustration! I am attempting to compile MOPAC 6.0 for the IBM RS-6000 and all I get are endless streams of error messages. Is there a kind soul who could provide the correct code, presumably by FTP, which would compile easier of the RISC sytem I use? My compiler is XLF. thanks in advance matt. ----------------------------------------------------------------------------- Matthew E. Harbowy Cornell U Chemistry Department Ithaca NY 14853 harbowy@chemres.tn.cornell.edu (or) ikf@vax5.tn.cornell.edu ----------------------------------------------------------------------------- --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Wed Aug 5 12:07:17 1992 Date: Wed, 5 Aug 1992 9:40:21 -0400 (EDT) From: CHALLACOMBE@BAEYER.CHEM.FSU.EDU Subject: HF-Limit Density To: CHEMISTRY@ccl.net Status: R Net, I am looking for a FORTRAN program to calculate accurate (HF limit) densities for small molecules. Programs using numerical HF or Slater type functions would be great. If the response is sufficient, I will post a summary to the net. Many thanks, Matt -------------------------------------------------- Matt Challacombe Program in Chemical Physics and the Supercomputer Computations Research Inst. Tallahassee, Fl. 32306 Challacombe@baeyer.chem.fsu.edu --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Wed Aug 5 13:08:43 1992 Date: Wed, 5 Aug 92 10:48:45 -0400 From: friedman@tammy.harvard.edu (Dawn Friedman) To: chemistry@ccl.net Subject: just one more thing... Status: R Ah, yes. In my previous G90 reply summary, I left out one question: If I do go to MCSCF, what becomes of the simple orbital picture I'm trying to substantiate? Is it possible for me to say whether the odd electron is in a pi or a sigma orbital? Is there a projection I can do over the determinants? --Dawn --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Wed Aug 5 14:09:36 1992 Date: 5 Aug 92 10:08 LCL From: PA13808%UTKVM1.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU To: CHEMISTRY@ccl.net Subject: BITNET mail follows Status: R MM2 FORCEFIELD PARAMETER DATABOOK I deduce from some of the recent mail that there is a need for a listing of molecular parameters. A flier with the above title describes a book meeting some of these requests appeared in my mail re cently.It contains "more than 250 MM2 Force field parameters calculated and compiled at the Tsukuba Research Center of Mitsubishi Petrochemical company". It contains nearly 500 pages and has a full discussion of how the parameters were obtained. It looks as if it discusses literature valuesin some detail discussing the estimation process and degree of approximation. I would imagine this book would be invaluable to workers in this field. Now for the bad news. The book is published by MARTECH ,541 Tokyo Club bldg. Kasumigaseki 3-2-6 Chiyoda-ku Tokyo 100 Japan.and is priced at ONE THOUSAND($1000.00)USA DOLLARS.Also it has a condition ofsale that it not be"lent,hired out or otherwise lent out or otherwise circulated " Oh yes reading the fine print I see that when publishing work using parameters from the book "He(she) shall not make public the parameter it itself"(More on that later). Well I just thought that if your are rich and/or your time is a valuable commodity you might like to know about it. Since it would appear the book quotes data from the literature I would like to hear from anyone who has given written permission to THEM to publish their lit data in such a book.The copywrite system works both ways. JEB(PA13808 at UTKVM1) --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Wed Aug 5 16:10:18 1992 Date: Wed, 5 Aug 92 10:36:11 -0400 From: friedman@tammy.harvard.edu (Dawn Friedman) To: chemistry@ccl.net Subject: g90 error/SCF convergence Status: RO Thank you to the many who told me about "limit coredumpsize 0" -- among others, David Bernholdt at the QTP, Robert Jones at Thinking Machines, Terry Coley at Caltech, and Nico van Eikema Hommes at Erlangen. Thanks to the "limit" command, I now know I won't be getting giant core dumps. The SCF convergence problem was less popular, and I'm still a little confused by the responses, so I thought I'd report them here and see if they can be brought into agreement. Margot at eorgia Tech says that UHF may not be a good wavefunction for this radical anion, and I may need to go to MCSCF or CASSCF (both in Gaussian, though I see that you need G92 for analytical CASSCF second derivatives for frequencies and force constants.) Even if I manage to overcome the convergence problems at UHF, if those problems are chronic, the UHF wavefunction I obtain may be junk -- unstable or otherwise poor. Well, the convergence problems _are_ chronic and the neutral molecule wavefunction back at 3-21g* is unstable, which seems ominous. Nico van Eikema Hommes suggests that I may be getting an error he's familiar with, in which the SCF converges but then the "last cycle without DIIS" fails -- a problem that extended basis sets like 6-311++g** are prone to because of linear dependency. The result looks like: SCF DONE E(UHF)=[number] after nn cycles Convergence failure, run terminated This is indeed what I'm seeing. He suggests that I try the option IOP(5/20=2) which avoids that last cycle without DIIS. (And notes that if I'm using SCF=direct, I should use SCF=(DIRECT,NOVARACC) as well.) "A more dangerous technique" is to force the optimization to continue despite the convergence failure, using IOP(5/13=1). This will help if it's the bad geometry that's causing the convergence failure, but it may also "yield nonsense." As for me, it's clear that the first step is to figure out the instability of the neutral molecule wavefunction, and I've had some advice about that, too, which I'll be looking at. But can someone provide a consensus on what to do about bad SCF convergence? That is, if I use one of the techniques to avoid the convergence problem, should I then test the stability of the resulting wavefunction? Many thanks, Dawn --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Wed Aug 5 17:10:32 1992 Date: Wed, 5 Aug 92 17:56:02 GMT From: jpj@lotus.medicine.rochester.edu (Jeffrey P. Jones) To: CHEMISTRY@ccl.net Subject: MOBOSOL BUG FIX Status: RO Hello: A bug has been reported and fixed for the MOBOSOL code when it is used with the envaq keyword. The envaq correction were only made for reaction coordinate calculations. This can be corrected by retrieving the new readmo.f file from crocus.medicine.rochester.edu. The code is in the jones directory. The compressed tar mobosol has the correction incorporated and a executable for SGI machines (monbo3). I would like to thank Vidana C. Epa for alerting us to the problem. It just goes to show that you get what you pay for (sometimes) ! ############################################################################## Surface Mail Jeffrey P. Jones U. of Rochester Department of Pharmacology 601 Elmwood Ave. Rochester, NY 14642 internet jpj@lotus.medicine.rochester.edu %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Wed Aug 5 17:58:34 1992 Date: Wed, 5 Aug 92 12:19:33 -0700 From: pat@mercury.aichem.arizona.edu (Pat Walters) To: chemistry@ccl.net Subject: HP plots from macro-model Status: R Hi, Has anyone been able to generate pen plots from macro-model. I know that macro-model will produce postscript files. Is there a program out there which converts postscript to HPGL? Is there any other way to do this? Thanks in advance, Pat _________________________________________________________________________ Pat Walters pat@mercury.aichem.arizona.edu Graduate Student Laboratory for Artificial Intelligence in Chemistry * Dept of Chemistry * * * University of Arizona, Tucson AZ 85721 * * * 602-621-6334 *** "At least its a dry heat" * _______________________________________________________*__________________ --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Wed Aug 5 20:08:00 1992 Date: Wed, 5 Aug 92 15:41:33 -0500 From: jerzy@tiger.JSUMS.EDU (Leszczynski) Status: R Dear Colleague: We are please to announce a workshop on CURRENT TRENDS IN COMPUTATIONAL CHEMISTRY. The symposium will cover all areas of Computational Chemistry as well as quantum chemistry . The workshop will be held at the Holiday Inn North, Jackson Mississippi on November 6 & 7, 1992. The format consists of a series of plenary lectures on Friday afternoon, Saturday morning, and afternoon followed by a banquet Saturday evening. In addition a welcoming reception and poster presentations are scheduled on Friday night. There will be talks covering applications as well as theory. We are planning to publish extended abstracts (up to 4 pages) of all invited talks and poster presentations. Enclosed are an Announcement Poster, a registration form and a housing information. The deadline for registration and an abstract submission is September 30, 1992. Sincerely, Jerzy Leszczynski Address:Jerzy Leszcynski, Jackson State University, Dept of Chemistry, 1400 JR Lynch St., Jackson, MS - 39217. Phone: (601) 973-3482 Fax: (601) 973-3674. E-Mail : jerzy2@iris5.jsums.edu. PROGRAM The program will include invited papers and contributed posters in all areas of Quantum and Computational Chemistry. INVITED SPEAKERS George F. Adams US Army Ballistic Research Laboratory Jan Amlof University of Minnesota Rodney J. Bartlett University of Florida Christopher J. Cramer US Army Chemical Research Center Janet E. Del Bene Youngstown State University Yasujuki Ishikawa University of Puerto Rico William A. Lester, Jr. University of California, Berkeley Gerald Maggiora Upjohn Company Peter Politzer University of New Orleans Peter Pulay University of Arkansas Svein Saebo Mississippi State University Henry F. Schefer III University of Georgia Donald G. Truhlar University of Minnesota Registration form: Workshop on CURRENT TRENDS IN COMPUTATIONAL CHEMISTRY NOVEMBER 6 & 7, 1992, Jackson, Mississippi 1. NAME: 2. INSTITUTION AFFILIATION: MAILING ADDRESS: TELEPHONE: FAX: E-MAIL: 3. If you wish to present a poster, please indicate the title below. All abstracts are due Sepetember 30, 1992 (up to 4 pages in length, presenting author underlined, photo-ready quality, in duplicate) to ensure publication in the workshop Nateruaks, TITLE: AUTHORS: 4. Conference materials, banquet and reception fee, cofee and refreshments are included per paid participant. Make checks payable to : JACKSON STATE UNIVERSITY, Department of Chemistry, in accord with the fee structure listed below. Registration fee before September 30, 1992, $75.00 $------- Registration fee thereafter, $ 100.00 $------- Registration fee at student discount, $25.00 $------- 5. HOUSING: The organizers will not make housing reservations. In order to reserve a room at a special conference rate of $42.00 per room (occupancy 1-4, including complimentary continental breakfast) call Holiday Inn North, 5075 I-55 North, P.O. Box 16083 Jackson, MS 39206, (601) 366-9411. The reservation should be arranged with the Holiday Inn before October 20, 1992. I do ------- do not ------- plan to stay at the Workshop hotel. ----------------- signature Please type all entries and return to Jerzy Leszczynski, Department of Chemistry, Jackson State University. P.O.Box 17910, Jackson, MS 39217. --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net ---