From acroft@chemistry.adelaide.edu.au Sun Dec 5 01:53:08 1993 Received: from pene.science.adelaide.edu.au for acroft@chemistry.adelaide.edu.au by www.ccl.net (8.6.4/930601.1506) id BAA12119; Sun, 5 Dec 1993 01:06:50 -0500 Received: by pene.science.adelaide.edu.au (5.61+IDA+MU/UA-5.26) id AA01687; Sun, 5 Dec 1993 16:36:49 +1030 From: Anna Croft Message-Id: <9312050606.AA01687@pene.science.adelaide.edu.au> Subject: Thanks To: chemistry@ccl.net Date: Sun, 5 Dec 1993 16:36:49 +1100 (EST) X-Mailer: ELM [version 2.4 PL3] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Length: 291 Thanks to everyone who replied to my request on Cartesians to Zmatricies. The information I have received was most valuable. Anna Croft /* ** #include ** #define CHEMIST acroft@chemistry.adelaide.edu.au ** #define UNIVERSITY university_of_adelaide */ From ole.swang@kjemi.uio.no Sun Dec 5 07:53:13 1993 Received: from pat.uio.no for ole.swang@kjemi.uio.no by www.ccl.net (8.6.4/930601.1506) id HAA12737; Sun, 5 Dec 1993 07:03:36 -0500 From: Received: from ulrik.uio.no by pat.uio.no with local-SMTP (PP) id <05418-0@pat.uio.no>; Sun, 5 Dec 1993 13:03:32 +0100 Received: by kelvin.uio.no ; Sun, 5 Dec 1993 13:03:31 +0100 Date: Sun, 5 Dec 1993 13:03:31 +0100 Message-Id: <9312051203.AAkelvin11465@kelvin.uio.no> To: eloranta@tukki.jyu.fi Cc: chemistry@ccl.net In-Reply-To: Jussi Eloranta's message of Sat, 4 Dec 1993 20:08:23 +0200 (EET) <199312041808.AA18794@tukki.jyu.fi> Subject: amsterdam dft code... (questions) ADF has geometry optimization using gradients. Also, it calculates vibrational frequencies. It is commercial, but the price is reasonable for academic users (we paid 1500 NLG, which is about 1000 USD). It runs on several different makes of computers (we use it on a Cray and on IBM workstations, but several other platforms are supported as well). I have been told that they work on a parallellized version. Basis sets for all atoms up to Lawrencium (no. 103) are included, and scalar relativistic effects can be taken into account. Ole Swang From d3f012@pellucidar.pnl.gov Sun Dec 5 10:53:15 1993 Received: from pnlg.pnl.gov for d3f012@pellucidar.pnl.gov by www.ccl.net (8.6.4/930601.1506) id KAA12956; Sun, 5 Dec 1993 10:48:58 -0500 From: Received: from pellucidar.pnl.gov (130.20.182.74) by pnlg.pnl.gov; Sun, 5 Dec 93 07:46 PST Received: by pellucidar.pnl.gov (920330.SGI/920502.SGI) for @pnlg.pnl.gov:chemistry@ccl.net id AA13128; Sun, 5 Dec 93 07:46:44 -0800 Date: Sun, 5 Dec 93 07:46:44 -0800 Subject: EISPACK code in C To: chemistry@ccl.net Message-id: <9312051546.AA13128@pellucidar.pnl.gov> X-Envelope-to: chemistry@ccl.net Can anyone tell me if EISPACK routines are available in C ? Mark ************************************************************************** Mark A. Thompson Sr. Research Scientist email: d3f012@pnlg.pnl.gov Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory voice: 509-375-6734 PO Box 999, Mail Stop K1-90 Richland, WA. 99352 Argus available via anonymous ftp from pnlg.pnl.gov (130.20.64.11) (in the argus directory). Download the README file first. Disclaimer: The views expressed in this message are solely my own and do not represent Battelle Memorial Institute, Pacific Northwest Laboratory, or any of its clients. ************************************************************************** From news@nntp-server.caltech.edu Sun Dec 5 12:53:17 1993 Received: from punisher.caltech.edu for news@nntp-server.caltech.edu by www.ccl.net (8.6.4/930601.1506) id MAA13309; Sun, 5 Dec 1993 12:35:13 -0500 Received: from gap.cco.caltech.edu by punisher.caltech.edu with SMTP (8.6.4/DEI:4.41) id JAA15008; Sun, 5 Dec 1993 09:35:11 -0800 Received: by gap.cco.caltech.edu (4.1/DEI:4.41) id AA08875; Sun, 5 Dec 93 09:35:09 PST To: mlist-chemistry@nntp-server.caltech.edu Path: nntp-server.caltech.edu!rpm From: rpm@bach.wag.caltech.edu (Richard P. Muller) Newsgroups: mlist.chemistry Subject: SUMMARY: Modeling Drug Binding Date: 5 Dec 93 09:35:08 Organization: Materials Simulations Center Lines: 183 Distribution: mlist Message-Id: Nntp-Posting-Host: bach.wag.caltech.edu Here's a summary of responses to my question on modeling drug binding. My initial request was... > > I'm interested in learning about work done to model drug binding sites > in biological systems. I remember hearing about a computer program > which designs potential drugs given a binding site, but I can't > remember anything else about it. Can anyone give me a reference for a > good review article in this field. I'll summarize if there's interest. > > Rick > ...and here is a list of references I received. Thanks to all who took the time to respond. -------------------------------- Here is a summary of responses I received to a request for information about computer modeling of drug binding sites in biological systems. ----References---- (Most of these references are Author et al.) Bugg, Carson, & Montgomery, Scientific American, December, 1993. --- Bohm JCAMD 6, 61 Caflisch J Med Chem 36, 2142 Cohen J Med Chem 33, 883 Martin J Med Chem 35, 2145 Marshall TrendsPharmSci 9, 285 AnRevPharmTox 27, 193 Meng J. Comp. Chem 13, 503 Murco J. Med. Chem. 36, 1700 J. Comp Chem: 14, 1184 Richards Prot Eng 6, 133 Schoiket Science 259, 1445 ----Books---- Molecular Foundations of Drug Receptor Interatction P. M. Dean Cambridge U. Press, 1987 Reviews in Computational Chemistry, Volume 5 The Development of Computational Chemistry in the United States John D. Bolcer and Robert B. Hermann Applications of Post-Hartree-Fock Methods: A Tutorial Rodney J. Bartlett and John F. Stanton Population Analysis and Electron Densities from Quantum Mechanics Steven M. Bachrach Biological Applications of Electrostatic Calculations and Brownian Dynamics Simulations Jeffry D. Madura, Malcolm E. Davis, Michael K. Gilson, Rebecca C. Wade, Brock A. Luty, and J. Andrew McCammon Computer Simulation of Lipid Systems K. V. Damodaran and Kenneth M. Merz Jr. Distance Geometry in Molecular Modeling Jeffrey M. Blaney and J. Scott Dixon A Perspective of Modern Methods in Computer-Aided Drug Design Lisa M. Balbes, S. Wayne Mascarella, and Donald B. Boyd Compendium of Software Donald B. Boyd ----Programs---- LUDI Biosym Dr. H.J. Boehm, BASF J.CAMD 6 1992 61 and 593 COSMIC Nottingham, Cambridge, London Dr. J.G. Vinter, Cambridge Morley et al. J.CAMD 5 1991 475 GRID Molecular Discovery Ltd., West Way House, Elms Parade, Oxford OX2 9LL UK Dr. P. Goodford, Oxford J.Med.Chem. 23 1985 849 DOCK UCSF dr. I. Kuntz, UCSF des Jarlais et al. J.Med.Chem. 29 1986 2149 GROW Upjohn Company dr. W.J. Howe, Upjohn Moon et al. Proteins: Struct. Funct. Genet. 11 1991 314 HOOK York, Harvard, possibly Molecular Simulations Inc.? Dr. R. Hubbard, York MCSS Harvard, possibly Molecular Simulations Inc.? dr. M. Karplus, Harvard Miranker et al. ? CoMFA Tripos Associates, 1699 Hanley Road, St. Louis, Missouri 63144 Also Receptor and Leapfrog available. dr. R. Cramer III, Tripos JACS 110 1985 5959 APEX Biosym dr. V. Golender Golender and Rosenblit Logical and Combinatorial Algorithms for Drug Design Research Studies Press, Letchworth 1983 ALADDIN Daylight Chemical Information Systems, 3951 Claremont St., Irvine, CA 92714 dr. Y. Martin, Abbott van Drie et al. J.CAMD 3 1989 225 CAVEAT, ILIAD, TRIAD UCB dr. P. Bartlett, UCB Bartlett et al. in Chemical and Biological Problems in Molecular Recognition ? SPERM Organon International dr. V. van Geeresteijn, Organon JCAMD 1991? AAA Washington University, St. Louis dr. G. Marshall, WU CMD Marshall et al. Comp.Ass.Drug Design.Symp. 112 1979 Ch.9 205 MTD Faculty of Pharmacy, Timisoara, Rumania dr. Z.Simon Simon et al. J.Theor.Biol. 66 1977 485 ?? Cambridge dr. P. Dean, Cambridge Chau and Dean J.CAMD 1992 several articles ?? Nishibata and Itai Tetrahedron 47 1991 8985 Thanks to Drs. Kapenga, Boyd, Kleijwegt, Martin, Shands, Raman, Xiao, Yuan, Moret, Villar -- ---------+---------+---------+---------+---------+---------+---------+ Richard P. Muller rpm@wag.caltech.edu Beckman Institute 139-74 (818) 395-2722 Office California Institute of Technology (818) 568-9484 Home Pasadena, California 91125 (818) 585-0918 FAX From davide@stinch0.csmtbo.mi.cnr.it Sun Dec 5 12:58:20 1993 Received: from stinch0.csmtbo.mi.cnr.it for davide@stinch0.csmtbo.mi.cnr.it by www.ccl.net (8.6.4/930601.1506) id MAA13291; Sun, 5 Dec 1993 12:26:24 -0500 From: Received: by stinch0.csmtbo.mi.cnr.it (911016.SGI/911001.SGI) for chemistry@ccl.net id AA05095; Sun, 5 Dec 93 18:11:13 GMT Date: Sun, 5 Dec 93 18:11:13 GMT Message-Id: <9312051811.AA05095@stinch0.csmtbo.mi.cnr.it> To: chemistry@ccl.net Subject: ESR spectra simulation : summary Some time ago I inquire about ESR spectra simulation software. This are the answers : Thank you all Davide From: dsingh@maple.circa.ufl.edu Reply-To: dsingh@ufcc.ufl.edu Subject: RE: software for ESR spectra simulation. ref: Spectral Simulation, I have found that the programme by Dennis Chasteen, Univ. of New Hampshire (I think) is extremely good. It is available gratis. His address may be obtained from any recent ACS directory of Graduate Research. I only have at the moment one reference on his work, but it is seminal: D. Chasteen, R. J. Bloch, B. R. Rogers, M. W. Hanna J. Amer. Chem. Soc. v 95, 1301 (1973). Good luck! david singh From: Jussi Eloranta Subject: Re: software for ESR spectra simulation. >I would like to know which software is available to simulate >ESR spectra for known structures of transition metal complexes. > Well, as for every esr simulation you have to know the hfc's. And when you have this information then you can simulate the epr spectrum. The suitable programs, for example, have been written by the researches at the free univ. of berlin (these programs are also available from epr.chem.jyu.fi, anon. ftp). Also I'm writing an epr spectrum library (of C functions) but that is not ready for distribution yet. Ab initio methods for calculating hfs's give *very* bad results. Even for small molecules. This is because you would need the wave function value at the nucleus (where the operator has a singularity). One interesting method for solving HF equations are FEM based methods but that requires quite a bit of work (don't have time for that...) If you find out anything more, please let me know too. Regards, Jussi Eloranta ps. I'm mainly interested in Fe-proteins and Fe-anthracycline complexes with g-values around 4.3. Following this last suggestion I found this: Free University of Berlin, Organic Chemistry Software for EPR/ENDOR spectroscopy (Electron Spin Resonance) is available by anonymous ftp WITHIN EUROPE from: methan.chemie.fu-berlin.de (130.133.2.81) directory: pub/science/epr see the README file. (C) Copyright: Dr. Burkhard Kirste, Institut fuer Organische Chemie, Freie Universitaet Berlin, Takustrasse 3, D-1000 Berlin 33, Germany E-Mail: kirste@kristall.chemie.fu-berlin.dbp.de kirste@methan.chemie.fu-berlin.de The programs may freely be used and distributed by the scientific community, provided that the copyright notice is not removed. The programs may also be modified to meet personal requirements. The programs may not be sold or used commercially. There is no warranty whatsoever, regarding proper function of the programs, errors, or any damage they might cause; i.e., the user takes full responsibility. Current programming is done in C. The programs have been compiled with Turbo C (TC 2.0 on IBM-PC/AT and Atari ST) and UNIX C. Most of them have been in use for years, there are occasional updates. The distribution contains the FULL SOURCE CODE. Most of it is in C, for program VIEW there is also an old Turbo Pascal version. Also included is (mostly old) Fortran 77 code of several programs; this is no longer supported. Binaries for IBM-PC/AT are provided (subdirectory PC). An arithmetic coprocessor is strongly recommended and mandatory for some of the programs (data, eprftsm, hffits, polft, polyn). Unfortunately there is not much documentation, except for eprft.doc. CONTENTS data analysis of EPR and ENDOR spectra eprft simulation and least-squares fit of isotropic EPR spectra eprftsm fit of EPR spectra: Monte Carlo, Simplex, Marquardt hffit fit of isotropic EPR spectra with Mi-dependent linewidths hffit2 fit of isotropic EPR spectra with arbitrary linewidths manip manipulation of spectral data files polft fit of EPR powder spectra (constant linewidths) polyn simulation of EPR powder spectra view display spectra (IBM PC/AT only) Data formats: binary (16-bit integers) or ASCII (-32768..32767), amongst others; only y-values are to be provided. - BKi -- |~| Freie Universitaet Berlin, Institut fuer Organische Chemie / \ Burkhard Kirste kirste@kristall.chemie.fu-berlin.dbp.de /FUB\ Takustrasse 3, D-1000 Berlin 33 UUCP: kirste@fub.uucp `---' Telefon: (030)838-6484 Telefax: (030)838-5163 ************************************************************************** Among the files there is a collection of informations about many different programs related to ESR updated to march 1991. The file is called database.zip (DOS compressed file) and is available under : pub/science/epr/msdos ------------------------------------------------------------------- Davide M. Proserpio - Istituto di Chimica Strutturistica Inorganica Universita' di Milano, Via Venezian, 21 - 20133 Milano, Italy phone +39-2-70635120 fax 70635288 - davide@stinch0.csmtbo.mi.cnr.it -------------------------------------------------------------------