From hcj@gull.uncc.edu Mon Sep 20 20:57:15 1993 Date: Tue, 21 Sep 93 00:57:15 -0400 From: hcj@gull.uncc.edu (Harry C. Johnson) Message-Id: <9309210457.AA00944@gull.uncc.edu> To: GKING@arserrc.gov Subject: Re: C++ compiler There is a C++ compiler by GNU that is public domain. The anonymous ftp site is prep.ai.mit.edu. I think it should work on an SGI or RS/6000, but I have never tried it. -Harry From burkhart@goodyear.com Tue Sep 21 05:04:50 1993 Date: Tue, 21 Sep 93 09:04:50 -0400 From: burkhart@goodyear.com (Craig W. Burkhart) Message-Id: <9309211304.AA05097@rds325> To: chemistry@ccl.net Subject: PD C++ The only public domain (actually, "copyleft") C++ compiler that I know of comes from the Free Software Foundation. The anonymous ftp address is prep.ai.mit.edu. You will find all sorts of variants: ANSI C, Objective C++, and so on. I have implemented these on both Sparc 10 and SGI Personal Iris platforms. They seem to work in that I have compiled and run most of the GNU software (of the C variety) using these tools. This includes the Emacs LISP kernel. All seem to work normally. -------------------------------------------------------------------------- Craig W. Burkhart, Ph.D Senior Research Chemist E-mail: cburkhart@goodyear.com The Goodyear Tire & Rubber Co. Fone: 216.796.4431 Akron Technical Center Fax: 216.796.3947 Akron, OH 44309-3531 -------------------------------------------------------------------------- "Wine and friends must be old to be appreciated" - old Italian maxim -------------------------------------------------------------------------- From wgalazka@chem.uw.edu.pl Tue Sep 21 15:50:13 1993 Organization: Department of Chemistry, University of Warsaw From: "Wojtek Galazka" Date: Tue, 21 Sep 93 14:50:13 +0100 Message-Id: <1560.wgalazka@zoolook.chem.uw.edu.pl_POPMail/PC_3.2.3_Beta_2> To: chemistry@ccl.net Subject: MOPAC sources - summary Hi ! Over three weeks ago I asked about MOPAC sources. Now I want to thank all who helped me, especially J. K. Labanowski and ZORAN P. ZDRAVKOVSKI. As I use Sun Sparcstation I found ouchem.chem.oakland.edu the best site, becase there were sources rewritten for SUN. However there was no ESP.F file, but this was not a problem. And In Europe on nic.funet.fi host, in directory /pub/sci/chem/qcpe /(or something similiar) one can find MOPAC files too. //////////////////////////////////////////////// // Wojciech Galazka // // // // Computer Center // // Chemistry Department, Uniwersity of Warsaw // // Pasteura 1, 02-093 Warsaw, Poland // //////////////////////////////////////////////// From BRICKNEL@che.und.ac.za Sat Sep 21 18:13:35 1993 Message-Id: To: chemistry@ccl.net From: BRICKNEL@che.und.ac.za Date: 21 Sep 93 16:13:35 +0200 (SAST) Subject: help with g92 Dear netters, I am running calculations on g92 on a HP system with 600MB capacity. The complex I'm running has 23 atoms.The problem I'm encountering is running out of disk space.I've done both a BSSE and a frequency calculation recently and have run out of space.I've done freq. and BSSE calc. on this particular complex (but in a different orientation)on our system before, without any problems.Apparently nobody else utilizes our disk space. I had problems running optimizations on this complex before,disk space being our problem.Then 2 weeks later I ran the job without any hassles.Is this a case of computer temperamentality? Also, should a BSSE calc. take up enormous amounts of space? My termination signal reads: erroneous write. write 901120 instead of 1048576 fd = 8 sh: 4006 abort Thanks Brad From PA13808%UTKVM1.BITNET@phem3.acs.ohio-state.edu Tue Sep 21 15:36:02 1993 Date: 21 Sep 93 10:35 LCL From: PA13808%UTKVM1.BITNET@phem3.acs.ohio-state.edu Subject: BITNET mail follows To: CHEMISTRY@ccl.net Message-Id: <01H37GX48RKO8X0KSU@phem3.acs.ohio-state.edu> It is difficult to answer your question without knowing more about the type of "CHARGE TRANSFER" complex your are interested in.If you are concerned with geometry it is probably better to forget the term charge transfer and to think of them as weak complexes held together by dispersion forces and dipole-dipole forces(MULTIPOLE-MULTIPOLE and induced multipole multipole forces really). Then you have a whole r of models available.Very few "CT complexes"involve much charge transfe r in the ground state, The CT excitation which characterises them is to an excited state in which an electron is transferred from a donor to an acceptor. For example many PI/PI* type complexes. The only ones which involve CT in ground state are those in which a lone pair interacts with a polarisable acceptor eg an amine complexing with the iodine molecule.(Characterised by a considerable dipole moment change in the ground state. General refs Theory of Molecular Interactions by I.G.KAPLAN(1986) Theoretical Models of chemical Bonding ed Z.B.Maksic PART 4 Theoretical Treatment of Large Molecules and Their Interactions (Springer Verlag 1991)see also part3 Molecular Spectroscopy, Electronic Structure and Intramolecular Interactions. (Springer Verlag1991 John E. Bloor (PA13808 at UTKVM1.UTK.EDU) From HARPER_RICHARD_W@Lilly.com Tue Sep 21 05:58:17 1993 Date: Tue, 21 Sep 1993 10:58:17 -0500 (EST) From: HARPER_RICHARD_W@Lilly.com Subject: PC/Workstation-based Draw Progs To: CHEMISTRY@ccl.net Message-Id: <01H37HKXS69U0000KU@INET.D48.LILLY.COM> Dear Netters, Several inquiries regarding drawing and display programs for PC's and workstations have appeared in the recent past. A nice overview can be found in The Scientist (August 23, 1993) on page 18 (Tools & Technology). If this periodical is not available to you let me know, and I will attempt to summarize. Dick ************************************ * Richard W. Harper, Ph.D. * * Eli Lilly & Company * * Lilly Research Laboratories * * Lilly Corporate Center * * Indianapolis, IN 46285-0444 * ************************************ * (317) 276-5990 Voice * * (317) 276-5187 Fax * * EMail HARPER_RICHARD_W@lilly.com * * Compuserve 73277,1777 * ************************************ From: HARPER RICHARD W (MCVAX0::WALTZ) To: VMS MAIL ADDRESSEE (IN::"CHEMISTRY@ccl.net") From shenkin@still3.chem.columbia.edu Tue Sep 21 08:27:06 1993 Date: Tue, 21 Sep 93 12:27:06 -0400 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <9309211627.AA05684@still3.chem.columbia.edu> To: hcj@gull.uncc.edu (Harry C. Johnson), GKING@arserrc.gov Subject: Re: C++ compiler > From: hcj@gull.uncc.edu (Harry C. Johnson) > > There is a C++ compiler by GNU that is public domain. The anonymous > ftp site is prep.ai.mit.edu. I think it should work on an SGI or > RS/6000, but I have never tried it. As long as people are posting publicly on this thread, let me mention that on SGI, you do need the extra-cost Iris Development Option to compile g++. The reason is that without the IDO, you do not get the /usr/include/*.h files you need. -P. ************************f*u*cn*rd*ths*u*cn*gt*a*gd*jb************************ Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ., New York, NY 10027; shenkin@still3.chem.columbia.edu; (212) 854-5143 ********************** Wagner, Beame, Screvane in '93! ********************** From d3e129@cagle.pnl.gov Tue Sep 21 02:46:16 1993 Date: Tue, 21 Sep 93 09:46:16 PDT From: d3e129@cagle.pnl.gov Subject: C++ compiler To: GKING@arserrc.gov Message-Id: <9309211646.AA02197@cagle.pnl.gov> |>Hello chem netters. I was wondering if there is such a thing as a public |>domain C++ compiler. I would be using it on an SGI Iris 4D/35 running |>IRIX 4.0.1 with the R2000A/R3000 processor chip. Thanks in advance. |> |>Greg |> |>==================================================================== |>Gregory King Internet: gking@arserrc.gov |>Eastern Reg. Res. Ctr., ARS, USDA Voice: (1) 215 233 6675 |>600 East Mermaid Lane Fax: (1) 215 233 6559 |>Philadelphia, PA 19118-2551 |>==================================================================== |> The GNU g++ tools are public domain and are very reasonable tools. C, C++, debugger, emacs C and C++ modes. The down side is that you sometimes have to build other GNU tools to get the particular one you want. The up side is that they usually work the first or second time and there is a great deal of net-help. The anonymous FTP site is prep.ai.mit.edu. You could also use archie to find other sites. ============================================================================= === Ricky A. Kendall === === Mail Stop K1-90 === === Molecular Science Software Group === === Theory, Modeling, and Simulation Program === === Molecular Science Research Center === === Pacific Northwest Laboratory === === Richland, WA 99352 === === Phone: (509) 375-2602 === === Fax: (509) 375-6916 === ============================================================================= ============================================================================= === All opinions are my own and not those of any other life form, === === living, dead or unknown === ============================================================================= ============================================================================= === Parallel computing is the way of the future === === Always was ........ always will be!!!!! === ============================================================================= ============================================================================= === === === Support the American Diabetes Association === === === ============================================================================= From jjurban@cbda6.apgea.army.mil Tue Sep 21 08:36:44 1993 Date: Tue, 21 Sep 93 12:36:44 EDT From: "Joseph J. Urban" To: chemistry@ccl.net Subject: Call for Abstracts Message-Id: <9309211236.aa25281@cbda6.apgea.army.mil> -------CALL FOR ABSTRACTS------- ----------SECOND NOTICE--------- Announcing a call for abstracts for a symposium to be held at the National Meeting of the American Chemical Society in San Diego, CA, March 13-18,1994 entitled: "COMPUTATIONAL ORGANIC CHEMISTRY" SPONSORS: ACS Divisions of Computers in Chemistry and Organic Chemistry CHAIRS: K.N. Houk (UCLA) and J.J. Urban (US Army ERDEC) FEATURED SPEAKERS WILL INCLUDE: N. L. Allinger U. of Georgia R. Bader McMaster Univ. C. Cramer Univ. of Minnesota J. Damewood Zeneca Pharmaceuticals G. Frenking Marburg J. Gao SUNY, Buffalo W. Jorgensen Yale J.A. McCammon Houston Q. McDonald Columbia L. Radom Canberra D. Salahub Montreal T. Stouch Bristol Myers-Squibb and many more... TO SUBMIT AN ABSTRACT: Send 4 copies of a 150-word abstract (original on ACS abstract form) by Oct. 29, 1993 to one of the chairmen: J.J. Urban U.S. Army Edgewood Research, Development & Engineering Center SCBRD-RTC (Bldg. E3160) Aberdeen Proving Ground, MD 21010-5423 410-671-3332 K.N. Houk Department of Chemistry and Biochemistry University of California, Los Angeles 405 Hilgard Ave. Los Angeles, CA 90024-1569 From mn1@helix.nih.gov Tue Sep 21 10:03:09 1993 Date: Tue, 21 Sep 93 14:03:09 -0400 From: mn1@helix.nih.gov (M. Nicklaus) Message-Id: <9309211803.AA24708@helix.nih.gov> To: CHEMISTRY@ccl.net Subject: SUMMARY: Elementary Texts on Molecular Mechanics Dear Net-Workers, A few weeks ago I posted the following QUESTION ======== We recently had a summer student here who is a senior high school student and who asked me about an introduction to molecular mechanics. Everything I could come up with, including the four volumes of "Reviews in Computational Chemistry" by Lipkowitz and Boyd, proved to be way beyond the level we were looking for (and therefore way beyond understanding)...... Hence my question: Does anyone know of a VERY ELEMENTARY introductory text on molecular mechanics, preferrably in the context of drug development? Below, I am summarizing the answers I got. I have slightly edited them to save space, but I haven't removed multiple references (especially to the 1982 J. Chem. Edu. paper by Boyd and Lipkowitz). Thanks to all who responded; and thanks especially to those who already sent me reprints. Marc Nicklaus ANSWERS ======= -------------------------------------------------------------------------- One of the best elementary sources that I have found is a 1982 by Boyd and Lipkowitz (J. Chem. Edu. 1982, 59, 269-274. Some sections may be too difficult for high school students, but on the whole it should give the student a "feel" for what is going on. Also, you might like to check out an article that Lou Allinger and I wrote in Reviews of Computational Chemistry (vol 2, Chapter 3). Some of the material might prove useful. Mike Cory and I wrote a review paper on molecular modeling that appears Encyclopedia of Pharmaceutical Technology (vol 3, 1991 by Marcel Dekker, Inc.). Another article that may prove to be useful is one by Hopfinger (J. Med. Chem. 1985, 28, 1133). Phil Bowen bowen@Mobius.chem.uga.edu -------------------------------------------------------------------------- Two suitable books might be: Quantum Mechanics, Ira N. Levine, 4th ed, pp 583-587, and A Handbook of Computational Chemistry, by Tim Clark; this latter book is a bit out of date (1985), and concentrates too much (by current standards) on input, but has a section on MMX. E. Lewars elewars@trentu.ca -------------------------------------------------------------------------- There is a program called HyperChem which is quite popular for the PC environment. We have the program here (although we mostly do ab initio), and I found that they have a book that is an excellant elementary intro to computational chemistry. The book specifically goes into Molecular Mechanics with a basic description suitable for an undergrad, or someone who is just getting introduced to the concepts. The book comes separate with the program package -- perhaps HyperChem would sell it to you individually. Also, Tim Clark has a book called "Handbook of Computational Chemistry" that has a very readable section on Molecular Mechanics. Matthew McNichols mmcnicho@Jade.Tufts.EDU -------------------------------------------------------------------------- A "classic" monograph is Ulrich Burkert and Norman L. Allinger, Molecular Mechanics, ACS Monograph 177, American Chemical Society, Washington, D.C., 1982 (about 340 pages). It contains mainly text, but basic equations for the force field, minimization, etc. are given. This part is about 75 pages. The rest of the book contains experimental results for different chemical classes. I don't know is this too difficult for your student, but it contains the basics of MM. Raimo Uusvuori Raimo.Uusvuori@csc.fi -------------------------------------------------------------------------- Maybe Allinger s book is better. Also the Biosym manual is supposed to be pretty good. Yvonne Martin MARTIN@cmda.abbott.com -------------------------------------------------------------------------- I might recommend the following two books: "A Handbook of Computational Chemistry" by Tim Clark, Wiley & Sons, 1985. "Computational Chemistry Using the PC", By Donald Rodgers, VCH, 1991. Both have pretty good explanations of the technique and include some hands-on practical advice in using the programs. Rodgers also wrote a couple of introductory papers in American Laboratory a couple years back that may be useful. Greg Durst gdurst@dowelanco.com -------------------------------------------------------------------------- Here's what I was really looking for, a paper by Boyd & Lipkowitz on the molecular mechanics foundations in a easy reading format... D. Boyd & K. lipkowitz, J. Chem. Ed., 59, (1982), pp269-274. and P. Cox, J. Chem. Ed.,59, (1982), pp275-277. Greg Durst gdurst@dowelanco.com -------------------------------------------------------------------------- I've found two good "intro to MM" references to be "Molecular Mechanics, The Method and its Underlying Philosophy" by D. B. Boyd and K. B. Lipkowitz in J. Chem Ed., Vol 59 # 4, pp 269-274, April 1982 and "Molecular Mechanics, Illustration of its Application" by P. J. Cox, J. Chem. Ed., Bol 59, #4, pp 275-278, April 1982. No real applications to medicinal chemistry are discussed, however. Gary Meier gmeier@ncsa.uiuc.edu -------------------------------------------------------------------------- you might try "Conformational Properties of Macromolecules" by A. Hopfinger Academic press, or A Handbook of COmputational Chemistry", by Tim Clark, Wiley ?????? nmdl@rlmtc.ENET.hcc.com -------------------------------------------------------------------------- You might try "Computer Software Applications in Chemistry" by Peter C. Jurs. It covers a lot of areas but does have one chapter on molecular mechanics. Very elementary. Jeff Nauss nauss@ucmodl.che.uc.EDU -------------------------------------------------------------------------- Some people have found the following article a useful tutorial for beginners. "Molecular Mechanics. The Method and Its Underlying Philosophy." D. B. Boyd and K. B. Lipkowitz, J. Chem. Educ., 59, 269-274 (1982). BOYD DONALD B BOYD_DONALD_B@Lilly.com -------------------------------------------------------------------------- There was an article in J. Chem. Ed. sometime in 1982, I believe. I think the author was Don Boyd, or maybe Kenny Lipkowitz or both of them. Sorry I can't be more specific, but I don't have it in my office. This article is probably exactly the thing you are looking for, although it didn't get into drug design as I recall. If you have a big library handy, see if you have "Comprehensive Medicinal Chemistry", edited by Corwin Hansch and John Sammes. In vol 4 (Quantitative Med Chem), I have a paper with Peter Kollman on Molecular Mechanics and Drug Design. I tried to keep the math and physics to a minimum. One thing that I can say is that molecular mechanics by itself is not very useful in the field of drug design. As a component of the overall drug design process, it is quite important, however. The paper is kind of old, so the drug design part of it may be a little stale. George Seibel seibelgl@smithkline.com -------------------------------------------------------------------------- I suggest that you review articles from J. Chem. Education. In specific I refer to 'Molecular Mechanics The method and its underlying philosophy', vol 59, #4 1982 pp 269-274. and the following article (more complex) 'Molecular Mechanics Illustrations of it application', 59,4, 1982, pp 275-276. I suspect there may be more recent J. Chem. Ed. articles as well. Thomas Pierce THPierce@RohmHaas.Com -------------------------------------------------------------------------- ------------------------------------------------------------------------ Marc C. Nicklaus, Ph.D. Lab. of Medicinal Chemistry e-mail: mn1@helix.nih.gov National Cancer Institute, NIH Phone: (301) 402-3111 Bldg 37, Rm 5B29 Fax: (301) 496-5839 Bethesda, MD 20892 ------------------------------------------------------------------------ From JKONG@ac.dal.ca Tue Sep 21 12:33:14 1993 Date: Tue, 21 Sep 1993 15:33:14 -0300 From: JKONG@ac.dal.ca Subject: Re: Help wnated: file system consistancy To: chemistry@ccl.net Message-Id: <01H37R75XK1E000B5Y@AC.DAL.CA> Dear netters, I posted a question yesterday about filesystem consistancy. I just got an answer from a comp. prof. here. The problem is the files I moved out are still opened by a suspended process. I suspended that process to free some space but apparently I have to kill the process to actually get the space. Just "mv" doesn't work. Jing From raman@bioc01.uthscsa.edu Tue Sep 21 09:44:26 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9309211944.AA25805@bioc01.uthscsa.edu> Subject: Re: How to join the Biophysical Society To: xu@lisboa.ks.uiuc.edu Date: Tue, 21 Sep 1993 14:44:26 -0500 (CDT) Dong: > that we become a student/postdoc member of the Biophysical Society. Could > someone tell me how we can join it? Thanks a lot! Please contact: Emily Gray Executive Director Biophysical Society Office 9650 Rockville Pike Bethesda MD 20814 Tel: 301-530-7114 FAX: 301-530-7133 Bitnet: biophys@gunbrf Dues are: $100 for regular and $15 for student members. If you are planning on presenting an abstract or a talk then your membership should be processed prior to Oct 15., 1993. Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry c.raman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From jaeric@mtcamm.monsanto.com Tue Sep 21 10:31:26 1993 From: Jon A. Erickson Message-Id: <9309212031.AA26535@mtcamm.monsanto.com> Subject: Re: help with g92 To: chemistry@ccl.net (OSU Comp. Chem. List) Date: Tue, 21 Sep 93 15:31:26 CDT > I am running calculations on g92 on a HP system with 600MB capacity. > The complex I'm running has 23 atoms.The problem I'm encountering > is running out of disk space.I've done both a BSSE and a > frequency calculation recently and have run out of space.I've done > freq. and BSSE calc. on this particular complex (but in a different > orientation)on our system before, without any problems.Apparently > nobody else utilizes our disk space. Have you tried using the direct options? This feature is designed for running large molecules with limited disk space. The new orientation may have broken symmetry, which may require more space. > I had problems running optimizations on this complex before,disk > space being our problem.Then 2 weeks later I ran the job without any > hassles.Is this a case of computer temperamentality? ???? > Also, should a BSSE calc. take up enormous amounts of space? Using ghost functions shouldn't take up any more space than normal. -- ################################################################ # Jon Erickson e-mail: jaeric@mtcamm.monsanto.com # # Monsanto Company, U3E phone: (314) 694-1511 # # 800 N. Lindbergh Blvd. FAX: (314) 694-1080 # # St. Louis MO, 63167 # # # # What is a magician but a practising theorist? # # -- Obi-Wan Kenobi # ################################################################ From rrk@iris3.chem.fsu.edu Tue Sep 21 13:12:56 1993 Date: Tue, 21 Sep 93 17:12:56 -0400 From: rrk@iris3.chem.fsu.edu (Randal R. Ketchem) Message-Id: <9309212112.AA16316@iris3.chem.fsu.edu> To: chemistry@ccl.net Subject: Re: How to join the Biophysical Society For information on the Biophysical Society: Emily M. Gray (301) 530-7114 FAX: (301) 530-7133 Internet: Biophys@NBRF.Georgetown.edu From hogue@canada.den.mmc.com Tue Sep 21 10:06:45 1993 Date: Tue, 21 Sep 93 16:06:45 MDT From: hogue@canada.den.mmc.com (Pat Hogue 1-2183) Message-Id: <9309212206.AA01410@canada.den.mmc.com> To: chemistry@ccl.net Subject: Two Perfluor compounds Can anyone help me find ionization potentials and refractive index or dielectric constant for perfluorodimethyl ether O(CF3)2 and perfluorodimethoxyacetal CF2(OCF3)2? Thanks in advance. Pat Hogue From CHAMANKHAH@sask.usask.ca Tue Sep 21 10:59:35 1993 Date: Tue, 21 Sep 1993 16:59:35 -0600 (CST) From: CHAMANKHAH@sask.usask.ca Subject: Looking for Chaya Duraiswami To: chemistry@ccl.net Message-Id: <01H37U7GCLSSA0V7MJ@SKYCAT.USask.CA> Hi netters; I'm sorry I'm sending this message. But I was unsuccessful to find the mailing address of Chaya Duraiswami. Could I ask him to contact me as soon as possible? Thanks and sorry for inconvenience. Mahmood