From eloranta@tukki.jyu.fi Mon Feb 14 02:22:20 1994 Received: from tukki.jyu.fi for eloranta@tukki.jyu.fi by www.ccl.net (8.6.4/930601.1506) id BAA15404; Mon, 14 Feb 1994 01:31:45 -0500 Received: by tukki.jyu.fi id AA24152 (5.67a/IDA-1.4.4 for chemistry@ccl.net); Mon, 14 Feb 1994 08:30:34 +0200 Date: Mon, 14 Feb 1994 08:30:34 +0200 From: Jussi Eloranta Message-Id: <199402140630.AA24152@tukki.jyu.fi> To: chemistry@ccl.net Subject: grid based methods using SCF Content-Length: 263 Hi, Does anyone have references or implementations for grid based methods (that is finite difference or finite element methods) for solving schrödinger equation using SCF? Esp. I'm interested in solvers which can cope with varying grid density. Thanks, Jussi From Leif.Laaksonen@pobox.csc.fi Mon Feb 14 03:22:20 1994 Received: from pobox.csc.fi for Leif.Laaksonen@pobox.csc.fi by www.ccl.net (8.6.4/930601.1506) id CAA15692; Mon, 14 Feb 1994 02:36:46 -0500 Received: from [128.214.46.163] (laaksone.csc.fi) by pobox.csc.fi with SMTP id AA05242 (5.65c8+/IDA-1.4.4 for ); Mon, 14 Feb 1994 09:36:37 +0200 Date: Mon, 14 Feb 1994 09:36:37 +0200 Message-Id: <199402140736.AA05242@pobox.csc.fi> X-Sender: laaksone@finsun.csc.fi Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable To: Jussi Eloranta From: Leif.Laaksonen@csc.fi Subject: Re: CCL:grid based methods using SCF Cc: chemistry@ccl.net Hi Jussi, I have some experience and references for the finite-difference approach. Please have a look at the following URL: http://www.csc.fi/lul/leif/publications.html Most of the quantum chemistry stuff is done using finite-differences. Cheers, -leif laaksonen >Hi, > >Does anyone have references or implementations for grid based methods >(that is finite difference or finite element methods) for solving= schr=96dinger >equation using SCF? Esp. I'm interested in solvers which can cope= with varying >grid density. > >Thanks, > >Jussi > >---Administrivia: This message is automatically appended by the= mail exploder: >CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net --= coordinator >MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net= (port 70 or 73) >Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net --= archive search ------------------------------------------------------------------- Leif Laaksonen | Center for Scientific Computing | Phone: 358 0 4572378 P.O. Box 405 | Telefax: 358 0 4572302 FIN-02101 Espoo | Voice Mail: 358 486257407 FINLAND | Mail: Leif.Laaksonen@csc.fi -------------URL: http://www.csc.fi/faces/leif.html---------------- New opinions are always suspected, and usually opposed, without any other=20 reason but because they are not already common. John Locke ------------------------------------------------------------------- From FLEMMING@dfhvax.nbi.dk Mon Feb 14 07:22:32 1994 Received: from nbivax for FLEMMING@dfhvax.nbi.dk by www.ccl.net (8.6.4/930601.1506) id HAA17779; Mon, 14 Feb 1994 07:07:59 -0500 From: Received: from DECNET-MAIL (FLEMMING@DFHVAX) by nbivax.nbi.dk (PMDF V4.2-13 #5783) id <01H8VKP3IP80AM5DQI@nbivax.nbi.dk>; Mon, 14 Feb 1994 13:08:00 +0100 Date: Mon, 14 Feb 1994 13:08:00 +0100 Subject: 2nd Eur. Congr. Pharmaceu. Sci. - Announcement To: chemistry@ccl.net Message-id: <01H8VKP3MZJMAM5DQI@nbivax.nbi.dk> X-VMS-To: CCL MIME-version: 1.0 Content-transfer-encoding: 7BIT * * * A N N O U N C E M E N T * * * ------------------------------------------------------------------------------- 2nd European Congress of Pharmaceutical Sciences 29th September - 1st October, 1994 Berlin, Germany ------------------------------------------------------------------------------- The 2nd European Congress of Pharmaceutical Sciences will take place in Berlin, Germany from September 29 to October 1, 1994. The programme will consist of 4 Plenary Trend Lectures and 14 Parallel Symposia on current topics in pharmaceutical sciences to be presented during three days. Short communications and poster sessions will complement the programme. The expected number of participants is approximately 1000. ------------------------------------------------------------------------------- Programme, registration form and further information can be obtained from: Apothekerhaus Carmerstrasse 3 10623 Berlin Germany Tel: (49) 30-3135091 Fax: (49) 30-3123081 ------------------------------------------------------------------------------- Congress Schedule Thursday September 29, 1994 Plenary Lecture J. Drews The evolution of biomedical science and the future of drug design Parallel Symposium 1 Enzymes as targets for drug development A.W. Alberts Recent approaches to cholesterol biosynthesis inhibition R.W. Hartmann Selective inhibition of steroidogenic P450 enzymes: Current status and future perspectives Parallel Symposium 2 Drug targeting D.J.A. Crommelin Targeting of peptide and protein drugs H.P. Merkle New aspects of pharmaceutical dosage forms for controlled drug delivery of peptides and proteins Parallel Symposium 3 Alternative methods to animal experimentation A. Cordier Strategy of using in vitro tests in preclinical safety testing B. Garthoff The use of transgenic animals in drug research Parallel Symposium 4 Pharmaceutical impact on chronic disease therapy R. Paoletti Combined drug therapy and the prevention of cardiovascular diseases J. Urquhart Compliance as a major determinant for the success of chronic drug treatment J.C. Aschoff Physostigmin for cerebellar ataxia's: The phantasies of a clinical neurologist and the real problems in developing a legalized therapeutic system (TTS) Friday September 30, 1994 Plenary Lecture E. De Clercq Trends in drug development for the treatment of AIDS Parallel Symposium 5 Receptor selectivity and drug development J.-C. Schwartz Molecular biology of receptors and drug design T.W. Schwartz Molecular mechanism of agonists and antagonists on neuropeptide receptors Parallel Symposium 6 Computer based methods in pharmaceutical sciences G. Folkers Modelling of ligand-protein interaction complexes as a basis of drug design Y.C. Martin Utility and challenges of 3D databases in new drug discovery Parallel Symposium 7 Overcoming biological barriers C. Laboisse Intestinal cell culture models H. Lennernas Gastrointestinal absorption mechanisms: A comparison between animal and human models Parallel Symposium 8 Non invasive techniques in drug development P. Hartvig PET-illuminating in vivo drug disposition C.G. Wilson Application of gamma scintigraphy to modern dosage form design M. Rudin In vivo magnetic resonance imaging and spectroscopy in pharmacological research: Applications to drug development and profiling Parallel Symposium 9 Pharmacoeconomics - a perspective on drug cost and drug benefit B. Joensson Health economics - what is it about? M.F. Drummond Health economic evaluation and reimbursement of pharmaceuticals G. Kobelt-Nguyen Health economics - an industry perspective Saturday October 1, 1994 Plenary Lectures J. Feijen The impact of biomaterials on pharmacists to drug research Y. Torud Contributions of European pharmacists to drug research Parallel Symposium 10 New approaches in drug synthesis P. Krogsgaard-Larsen Agonists, partial agonists and antagonists at GABA and glutamate receptors in Alzheimer's disease: Chemistry and pharmacology K.T. Wanner Chiral N-acyliminium ions as new tools in the asymmetric synthesis of CNS-active compounds Parallel Symposium 11 Antioxidants and cell protection S. Orrenius Intracellular oxidative processes and cell killing C. Galli Natural antioxidants, lipid peroxidation and platelet/leukocyte functions Parallel Symposium 12 Prediction of drug metabolism D.A. Smith Chemistry and enzymology: Their use in the prediction of human drug metabolism W. Taeschner Prediction of genetic variation of drug metabolism Parallel Symposium 13 Plant metabolites as models for modern drug research W.F. Fleck Benzo[a]naphthacenequinones from microorganisms as models of modern drug research W. Kubelka Constituents of higher plants as models for modern drug research M. Tanker Certain Anatolian plants and their constituents influencing drug disposition Parallel Symposium 14 New opportunities for near infrared (NIR) spectrometry in pharmaceutical and biomedical analysis C. van der Vlies The use of NIR spectrometry in the pharmaceutical control laboratory M. Josefson New opportunities with NIR spectrometry in the analysis of dosage forms R.A. Lodder NIR-Spectrometric imaging ------------------------------------------------------------------------------- The above announcement has been submitted to CCL by: Flemming Steen Jorgensen Associate professor, Ph.D. Royal Danish School of Pharmacy Department of Medicinal Chemistry Universitetsparken 2 DK-2100 Copenhagen Denmark Phone: +45 35 37 08 50 ext. 378 Fax: +45 35 37 22 09 If you need more information, you are welcome to contact me on: flemming@dfhvax.nbi.dk ------------------------------------------------------------------------------- From SAVARY@sc2a.unige.ch Mon Feb 14 11:23:03 1994 Received: from chx400.switch.ch for SAVARY@sc2a.unige.ch by www.ccl.net (8.6.4/930601.1506) id KAA19859; Mon, 14 Feb 1994 10:35:00 -0500 From: X400-Received: by mta chx400.switch.ch in /PRMD=switch/ADMD=arcom/C=CH/; Relayed; Mon, 14 Feb 1994 16:34:12 +0100 X400-Received: by /PRMD=SWITCH/ADMD=ARCOM/C=CH/; Relayed; Mon, 14 Feb 1994 16:33:49 +0100 X400-Received: by /PRMD=SWITCH/ADMD=ARCOM/C=CH/; Relayed; Mon, 14 Feb 1994 17:30:42 +0100 X400-Received: by /PRMD=SWITCH/ADMD=ARCOM/C=CH/; Relayed; Mon, 14 Feb 1994 17:30:32 +0100 X400-Received: by /PRMD=SWITCH/ADMD=ARCOM/C=CH/; Relayed; Mon, 14 Feb 1994 17:30:32 +0100 Date: Mon, 14 Feb 1994 17:30:32 +0100 X400-Originator: SAVARY@sc2a.unige.ch X400-Recipients: CHEMISTRY@ccl.net X400-MTS-Identifier: [/PRMD=SWITCH/ADMD=ARCOM/C=CH/;<01H8VRJ1IHJ6001291@sc2a.unige.c] X400-Content-Type: P2-1984 (2) Content-Identifier: algorithm for... Message-ID: <01H8VRJ1IHJ6001291@sc2a.unige.ch> To: CHEMISTRY@ccl.net Subject: algorithm for Cn axes X-Envelope-to: CHEMISTRY@ccl.net X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Dear CClers Is there an easy way (even complicated will do) to find the principal axes of symmetry of a given molecule knowing only the atoms coordinates, it is not only to be able to build internal coordinates (as MOPAC or other packages do) but to be of general use, (I think Spartan does it). Sorry if it is a FAQ. Francois Savary -------------------------------------------------------------- Francois Savary Department of Physical Chemistry University of Geneva 30, quai Ernest-Ansermet CH-1211 Geneva 4 phone : +4122 702 65 32 fax : +4122 702 65 18 e-mail : savary@sc2a.unige.ch -------------------------------------------------------------- From UNC4B2@plumbum.chemie.uni-bonn.de Mon Feb 14 13:24:53 1994 Received: from IBM.rhrz.uni-bonn.de for UNC4B2@plumbum.chemie.uni-bonn.de by www.ccl.net (8.6.4/930601.1506) id MAA21909; Mon, 14 Feb 1994 12:27:01 -0500 Message-Id: <199402141727.MAA21909@www.ccl.net> Received: from plumbum.chemie.uni-bonn.de by IBM.rhrz.uni-bonn.de (IBM VM SMTP V2R2) with TCP; Mon, 14 Feb 94 18:27:05 MEZ Received: from SNCHEMIE1/MERCURY by plumbum.chemie.uni-bonn.de (Mercury 1.1); Mon, 14 Feb 94 18:24:27 EST To: CHEMISTRY@ccl.net From: "Christoph Steinbeck " Organization: Dep. of Chemistry, Bonn Date: Mon, 14 Feb 1994 18:23:57 EST Subject: Drawing structure from connection table? Reply-to: steinbeck@uni-bonn.de Priority: normal X-mailer: WinPMail v1.0 (R2) Hi all, I need to draw chemical structures from connection tables, made by my program. In other terms, I need a 2D-Modelbuilder. I have no coordinates at all!!! Do you know of any program, which does that. I know some, but all are included to big, commercial packages and I need to get the source code to include it to my program. thanx, Chris -- Christoph Steinbeck (STEINBECK@UNI-BONN.DE) Abt. Prof. Breitmaier, Dep. of Chemistry, Univ. Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn 1, GERMANY Tel.: (49) 228 735669, Fax: (49) 228 735683 *** If life gives you a lemon - make lemonade! *** From smb@smb.chem.niu.edu Mon Feb 14 13:27:54 1994 Received: from mp.cs.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.6.4/930601.1506) id MAA23616; Mon, 14 Feb 1994 12:57:33 -0500 Received: from cz2.chem.niu.edu by mp.cs.niu.edu with SMTP id AA06228 (5.67a/IDA-1.5 for <@mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@ccl.net>); Mon, 14 Feb 1994 11:57:30 -0600 Received: from smb.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@ccl.net) id AA02856; Mon, 14 Feb 94 10:46:58 -0600 Received: by smb.chem.niu.edu (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:CHEMISTRY@ccl.net) id AA25521; Mon, 14 Feb 94 10:46:57 -0600 Date: Mon, 14 Feb 94 10:46:57 -0600 From: smb@smb.chem.niu.edu (Steven Bachrach) Message-Id: <9402141646.AA25521@smb.chem.niu.edu> To: CHEMISTRY@ccl.net Subject: Gordon Research Conference Information On-Line Hello Chem-netters, The Northern Illinois University Chemistry Gopher announces that the entire list of Gordon Research Conferences for 1994 are now available on-line through the gopher. To access this database, direct your gopher client to hackberry.chem.niu.edu port 70, then follow the Conference Listings, to Gordon Coferences directories. Also, if there are any conference organizers out there, we would be very pleased to add your conference announcements to our gopher server. Just e-mail the announcement to admin@hackberry.chem.niu.edu. We also are building a database of chemistry software. Any software developers (commerical and freeware) may e-mail a description of their product, platforms supported, and contact addresses to admin@hackberry.chem.niu.edu for inclusion in this databse. New developments will follow... Thanks Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 smb@smb.chem.niu.edu From tgm@SSD.intel.com Mon Feb 14 16:29:42 1994 Received: from SSD.intel.com for tgm@SSD.intel.com by www.ccl.net (8.6.4/930601.1506) id PAA25694; Mon, 14 Feb 1994 15:27:05 -0500 Received: from forseti.SSD.intel.com by SSD.intel.com (4.1/SMI-4.1) id AA06837; Mon, 14 Feb 94 12:26:33 PST Received: by forseti.SSD.intel.com (4.1/SMI-4.1) id AA26192; Mon, 14 Feb 94 12:26:30 PST Date: Mon, 14 Feb 94 12:26:30 PST From: "Timothy G. Mattson" Message-Id: <9402142026.AA26192@forseti.SSD.intel.com> To: chemistry@ccl.net Subject: Parallel Comp. Chem. Symposium Parallel Computing in Computational Chemistry ============================================= A symposium sponsored by the American Chemical Society Computers in Chemistry Division. Taking place during the Spring ACS meeting in San Diego, March 13- 18. Contact Tim Mattson of Intel Corp. Supercomputer Systems Division at tgm@ssd.intel.com if you have any questions about the symposium. 1. Applications of Parallel Computing (chair: T. Mattson) Sunday Morning, March 13. ----------------------------------------------------------- Direct Applications of Parallel GAMESS. M.S. Gordon, K. Baldridge, M. Schmidt, T. Windus, et.al. HYPERCHEM for Parallel Computers. N. S. Ostlund TITLE NOT AVAILABLE AT THIS TIME. C. Singh Computational Chemistry Applications for the IBM 9076 Scalable POWERPARALLEL System. M. Dupuis, S. Chin, S. Kandadai, F. Johnston, and J. Wong Parallel Implementation of the Spartan Electronic Structure Code. W.J. Hehre 2. Algorithms (chair: T. Mattson) Sunday Afternoon, March 13. --------------------------------- Object Oriented Implementation of Parallel ab initio Programs. C. L. Janssen and M. Colvin Fully Distributed Parallel Algorithms - Molecular Self Consistent Field Calculations. R. J. Harrison Parallel Molecular dynamics simulations of organic materials S. Plimpton and B. Hencrickson Fast Parallel Algorithms for Molecular Dynamics Simulation. A. Windemuth Parallel Approaches to Simulations of Solvated Biopolymers. C. L. Brooks and W. S. Young 3. Contributed Papers I, Mostly Ab initio (chair: T. Mattson) Tuesday Morning, March 15 -------------------------------------------------------------- Parallelization of a Multireference Configurations Interaction Program - the Parallel COLUMBUS Program, H. Lischka Implementation of GAMESS in Parallel. T. Windus M.W. Schmidt, K.K. Baldridge, J.A. Boatz, and M.S. Gordon Computational Chemistry on Fujitsu Parallel Computers: First Experiences. R. Nobes, F. S. Battle, R.A. Edberg, and P.A. Wielopolski Ab initial quantum chemistry on a workstation cluster. D. Turner, G. Trucks, and M. Frisch Efficient Parallel Computation of Electron Transfer Resonance Matrix Elements between GVB wavefunctions: Algorithm Design and Chemical Results. E. P. Bierwagon, T. R. Coley, and W. A. Goddard Parallel and Distributed algorithms for Pseudospectral Electronic Structure Calculations. D. Chasman, L. Wang, and R. Friesner 4. Contributed Papers II, Mostly MD (chair: S. Chin) Thursday Afternoon, March 17 ------------------------------------------------------ Biomolecular Structure Prediction with Parallelized PROTEAN2 and Neural Networks. J. A. Lupo, S. B. Fairchild, R. Pachter, and W. Adams Portable Molecular Dynamics Software for Parallel Computing, T. Mattson and G. Ravishanker Particle-Processor Assignment in Parallel Molecular Dynamics. W. Scott, F. Muller-Plathe, W. F. van Gunsteren Classical and Quantum Molecular Dynamics Simulation on Distributed memory Massively Parallel Computers. Z. Li, R. B. Gerber, and C.C. Martens Simulated Annealing simulations for Biopolymer Structure Prediction. Z. Wang, R. Pachter, and W. Adams Computational Chemistry on Kendall Square Research KSR/Series Computers. D. Zirl From axh14@cac.psu.edu Mon Feb 14 17:22:28 1994 Received: from milkman.cac.psu.edu for axh14@cac.psu.edu by www.ccl.net (8.6.4/930601.1506) id QAA26342; Mon, 14 Feb 1994 16:24:31 -0500 Received: from wilbur.cac.psu.edu by milkman.cac.psu.edu with SMTP id AA27033 (5.65c/IDA-1.4.4 for ); Mon, 14 Feb 1994 16:24:17 -0500 From: ARTHUR HOAG Received: by wilbur.cac.psu.edu id ; Mon, 14 Feb 1994 16:24:16 -0500 Date: Mon, 14 Feb 1994 16:24:16 -0500 Message-Id: <199402142124.AA27616@wilbur.cac.psu.edu> To: chemistry@ccl.net Subject: thermochemistry? I saw someones post regarding thermodynamic output from gaussian and have a couple questions my self concerning both gaussian and spartan. I wish to calculate delta G and delta G* for a reaction. I have already done the ab initio optimization and frequency calculation thus I have E in hartrees (I converted to kcal/mol as well), enthalpy at 298.15 K and 1 atm for vibration, translation, and rotation. I also have entropy at STP for vibration, rotation, and translation (I dont have a calculated electronic portion) To calculate the G's so I can calculate delta G's I use G=H-TS but, I need to know a couple things about H and S 1. Is H equal to E + Hvib + Hrot + Htrans? or do I need to add a pressure and volume correction? (the reaction is a fragmentation (loss of fluorine)) 2. Do I add the H's to a zero point corrected E or not? I assume uncorrected because Hvib should take care of that? 3. Is S=Svib + Srot + Strans? Sel is small? Do I also need to subtract at term such as nR(ln(nN)-1). I have tried this using my spartan output Svib +Srot +Strans but keep getting a negative absolute entropy which obiously doesnt make sense (note I am not talking about and entropy change). I am also interested in learning the common conventions for this sort of information. I have consulted my spartan and gaussian user guides with no luck. I have also consulted "ab initio molecular orbital theory" by Hehre, Radom, Schleyer, and Pople. As well as Exploring Chemistry with Electronic Structure Methods: A guide to using gaussian with no luck. If there are better sources for this info I would appreciate suggestions (excluding typical Statistical Thermodynamics books because these have not been clear to me. for example one included the nR(ln(nN-1) term while another did not. I think that is about all for now. Please send responses to axh14@wilbur.cac.psu.edu (and let me know if it is ok to direct further questions to you personally in response to your response) Arthur Hoag axh14@wilbur.cac.psu.edu ph 814-863-7980