From chemistry-request@ccl.net Tue Jun 9 00:47:32 1992 Date: Mon, 8 Jun 1992 20:24:14 -0600 From: roberson@hydroxide.chem.utah.EDU (Mark Roberson) Subject: Pseudopotentials To: CHEMISTRY@ccl.net Status: R Netters: Does anyone have helpful advice about using f-orbital polarization functions with SBK ECPs? In particular: i) What might be a good exponent for use with Osmium ii) Is there any truth to the rumblings that messing with an ECP basis invalidates the whole scheme iii) Are f-orbitals important anyway Thanx Mark roberson@hydroxide.chem.utah.edu From chemistry-request@ccl.net Tue Jun 9 04:11:31 1992 Date: Tue, 9 Jun 92 2:00:03 EDT From: Dongchul Lim Subject: how to get cartesian coordinates from one bond length and two bond To: chemistry@ccl.net (Computational Chemistry) Status: R In Gaussian92 zmatrix, a zmatrix card can be specified by a bond length, a bond angle, and a dihedral angle. Alternatively it can be specified by a bond length and two bond angles. I wonder if someone has a code to convert the latter form of zmatrix card to cartesian coordinates. A general format would be N N1 LENGTH N2 ANGLE1 N3 ANGLE2 SIGN where, cartesian coordinates of points N1,N2 and N3 are known, the length between N and N1 is LENGTH, the angle formed by N,N1,and N2 is ANGLE1, and the angle formed by N,N1,and N3 is ANGLE2. The last item SIGN specifies the sign of the triple vector product (N1-N).((N1-N2)x(N1-N3)). If this product is positive, SIGN is +1. If negative, SIGN is -1. What is to be computed is the cartesian coordinate of the point N. A subroutine like GETCART(N,N1,LENGTH,N2,ANGLE1,N3,ANGLE2,SGN) DOUBLE PRECISION N(3),N1(3),N2(3),N3(3),LENGTH,ANGLE1,ANGLE2 INTEGER SGN will be enough for me. Thanks. -dl ******************************************************************** * Dongchul Lim | Phone (203) 432-6288 * * Dept. of Chemistry, Yale Univ. | Email: lim@rani.chem.yale.edu * * 225 Prospect Street | (130.132.25.65) * * New Haven, CT 06511 | * ******************************************************************** From chemistry-request@ccl.net Tue Jun 9 11:10:07 1992 Date: 9 Jun 92 09:25 LCL From: PA13808%UTKVM1.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU Subject: BITNET mail follows To: CHEMISTRY@ccl.net Status: R STARTING TO USE GAUSSIAN X A good place to start, especially for the earlier Gaussian programms is Handbook of computational Chemistry: a practical guide to chem structure and energy calculations. by TIM CLARK. This book takes you through the input card by card. It also discusses with many examples the concept of the Z matrix. however a necessary prerequisite is to type and then proofread accurately. See the garbled quotation in the two communic. concerning this problem. Somethings just have to be exact to run or to be read. JEB From chemistry-request@ccl.net Tue Jun 9 12:37:53 1992 Date: Tue, 9 Jun 1992 08:51 CST From: C1790@slvaxa.umsl.EDU Subject: FINAL MEETING NOTICE To: CHEMISTRY@ccl.net Status: R ************** FINAL MEETING ANNOUNCEMENT **************** "THE 2ND ST. LOUIS GATHERING ON COMPUTER-AIDED MOLECULAR DESIGN" SATURDAY, JUNE 13, 1992 UNIV. OF MISSOURI-ST. LOUIS ST. LOUIS, MO 63121 REGISTRATION FEES: $50 ($25 FOR STUDENTS) NOTE: ON-SITE REGISTRATION WILL BE AVAILABLE ATTENDANCE: 125-150 PARTICIPANTS ARE EXPECTED SUMMARY OF PROGRAM: PRESIDING: PROFS. WILLIAM WELSH, UNIV. OF MISSOURI-ST. LOUIS AND GARLAND MARSHALL, WASHINGTON UNIV. IN ST. LOUIS "OVERVIEW OF MOLECULAR MECHANICS AND FORCE FIELDS" BY PROF. PHIL BOWEN, UNIVERSITY OF GEORGIA "OVERVIEW OF MOLECULAR DYNAMICS SIMULATIONS" BY DR. SHAWN HUSTON, WASHINGTON UNIVERSITY IN ST. LOUIS "PROTEIN HOMOLOGY MODELING" BY DR. NEENA SUMMERS, MONSANTO COMPANY, ST. LOUIS LUNCH, INCLUDING A "FILM FESTIVAL" OF COMPUTER-GENERATED SIMULATIONS "PATHWAYS FOR CONFORMATIONAL TRANSITIONS" BY PROF. RON ELBER, UNIVERSITY OF ILLINOIS-CHICAGO "MOLECULAR MODELS FROM NMR SPECTRA" BY DR. DENISE BEUSEN, WASHINGTON UNIVERSITY IN ST. LOUIS "POLYMER MODELING" BY DR. LAWRENCE DEBOLT, TRIPOS ASSOCIATES, INC., ST. LOUIS "ARTIFICIAL INTELLIGENCE AND NEURAL NETWORKS" BY DR. SAMUEL TERSIGNI, UNIVERSITY OF MISSOURI-ST. LOUIS POSTER SESSION WITH CATERED RECEPTION SPONSORS: UNIV. OF MISSOURI-ST. LOUIS WASHINGTON UNIVERSITY'S CENTER FOR MOLECULAR DESIGN SILICON GRAPHICS COMPUTERS TRIPOS ASSOCIATES, INC. AMERICAN CHEMICAL SOC., ST. LOUIS SECTION From chemistry-request@ccl.net Tue Jun 9 12:39:53 1992 Date: Tue, 9 Jun 1992 09:13 EST From: SPACE FOR RENT <00S0DAVIS@LEO.BSUVC.BSU.EDU> Subject: thanks To: chemistry@ccl.net Status: R Thanks to everyone who wrote me in answer to my question about running a single point calculation in gaussian 80, your advice and suggsetions where vary helpfull and helped me figure out what I had been doing wrong. Thanks, Spencer Davis From chemistry-request@ccl.net Tue Jun 9 17:44:56 1992 Date: Tue, 9 Jun 92 18:22:18 GMT From: "James P. Schmidt" Subject: NBO To: chemistry@ccl.net Status: R Here is the reply I recievde from Weinhold's group re: NBO The program NBO 3.0 and printed documentation are available through the Quantum Chemistry Program Exchange at Indiana University, Bloomington. The program manual describes the standard interface to Ampac. We also maintain a source program (.SRC code) of the latest available version on the GUEST account (password: JOYRIDE) of our VAX/VMS machine (node 128.104.26.10) for Telnet access. You can log into this account, change to the [.NBO] directory, and retrieve the files there, including the basic NBO.SRC program, the ENABLE.FOR "activator" (e.g., to generate the AMPNBO.FOR Ampac version from NBO.SRC), and the TechSet form of the program manual (the TechSet formatter is available through ACS Software at 202-872-4378). Andrew Holder at the Chemistry Department of the University of Missouri, Kansas City, is planning to market a version of the Dewar programs which includes NBO, so this is a third alternative you may consider. Thanks to those who replied to my query. Jim Schmidt University of Rochester Pharmacology Dept. jims@duce.medicine.rochester.edu From chemistry-request@ccl.net Tue Jun 9 18:30:19 1992 Date: 09 Jun 1992 16:25:42 -0400 (EDT) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: Computer languages To: chemistry@ccl.net Status: R I know that some Chemistry Departments allow programming languages such as FORTRAN or C to be used in place of a foreign language when students must meet a language requirement. I asked this question around a year ago, but now our department (at my urging) might consider allowing the same. So... Would anyone who is in a Department where programming languages are accepted please send me the text from your graduate student manual, catalog, etc., which describes your language requirement? I need to draft a proposal and I would like to see how other Departments word theirs. Email and/or faxed responses would be appropriate. Thanks in advance. Doug Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From chemistry-request@ccl.net Tue Jun 9 19:16:25 1992 Date: Tue, 9 Jun 92 15:20:46 PDT From: zheng@violet.berkeley.EDU Subject: Sparkles in MOPAC/AMPAC To: chemistry@ccl.net Status: R What would be the best way to change the size of sparkles in MOPAC/AMPAC? Any help will be appreciated. Ya-Jun Zheng From chemistry-request@ccl.net Tue Jun 9 22:34:20 1992 Date: Tue, 9 Jun 92 08:33:09 -0400 From: nobody@Kodak.COM Subject: More Fan mail... To: "chemistry@ccl.net"@Kodak.COM Status: R >From: NAME: Adi M. Treasurywala FUNC: Biophys. & Compu. Chem. TEL: (518)445-7042 To: "chemistry@ccl.net"@kodakr@mrgate@wpc Jan, I just wanted to echo Michael Lee's sentiment. This Net has CHANGED MY LIFE!! I have learned so much and feel very close to this "tribe" now. And its all because of your efforts behind the scenes!! THANKS. Adi Treasurywala. From chemistry-request@ccl.net Tue Jun 9 23:20:23 1992 Date: Tue, 9 Jun 92 20:47:07 EDT From: salahub@ERE.UMontreal.CA (Salahub Dennis R.) Subject: Re: Computer languages To: DSMITH@uoft02.utoledo.EDU (DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO) Status: R C'est absolument absurde de vouloir remplacer le francais, ou toute autre langue vivante, par le fortran ou le C!!!!! I wish I knew 20 more languages to state how repugnant this "equivalence" is. One may debate whether it is necessary to require a foreign language for a given degree (I know which side of the debate I would choose) but there is little to support the idea that learning Fortran has anything to do with learning French (or German, or Hindi...) in terms of acquired skills or the richness of experience the knowledge brings. It is probably futile to argue whether learning French or Fortran is more important; the two are different. Can other Netters put the above thoughts (the first two lines, or similar, or disparate...views) into other languages? (I'll offer a very good bottle of (French) champagne for a credible translation in Fortran (or C...). Bonsoir a tous! Nite-all! Dennis Salahub > > I know that some Chemistry Departments allow programming languages such as > FORTRAN or C to be used in place of a foreign language when students must > meet a language requirement. I asked this question around a year ago, but > now our department (at my urging) might consider allowing the same. So... > > Would anyone who is in a Department where programming languages are accepted > please send me the text from your graduate student manual, catalog, etc., > which describes your language requirement? I need to draft a proposal > and I would like to see how other Departments word theirs. Email and/or > faxed responses would be appropriate. > > Thanks in advance. > > Doug Smith > Assistant Professor of Chemistry > The University of Toledo > Toledo, OH 43606-3390 > > voice 419-537-2116 > fax 419-537-4033 > email dsmith@uoft02.utoledo.edu > -- ************************************************************ * Dennis Salahub SALAHUB@ERE.UMONTREAL.CA * * Departement de chimie Tel. (514) 343-6755 * * Universite de Montreal Fax (514) 343-2468 * * C.P. 6128, Succ. A N.B. new fax * * Montreal, Quebec H3C 3J7 92-01-30 * * Canada * ************************************************************