From chemistry-request@ccl.net Wed Jul 10 13:40:21 1991 Date: Wed, 10 Jul 91 12:30:02 CDT From: "Neil R. Kestner" To: CHEMISTRY@ccl.net Status: R Post Doctoral Position Available To Perform Quantum and Statistical Simulations One post doctoral fellow needed to continue studies on spectral properties of atoms and molecules in various fluids. Experience with ab initio as well as simulation methods is required. Experience with parallel computers is desired as codes will soon be adapted to run on LSU's MASPAr 4,000 node parallel computer and on Connection Machines. Also plan to use Intel computers on some projects as well. Salary could be up to $21,00 and appointment could run more than one year. Starting date could be as early as December. For details contact Neil R. Kestner Chemistry Department Louisiana State University Baton Rouge, LA 70803 BITNET: chkstr @ lsuvm Internet: chkstr @ lsuvm.sncc.lsu.edu FAX: (504)-388-3458 Phone: (504)-388-1528 From chemistry-request@ccl.net Wed Jul 10 20:42:31 1991 Date: Wed, 10 Jul 1991 15:32:17 PDT From: "W. Todd Wipke" To: tcm-online@secs.UCSC.EDU Subject: Recent Computer Chemistry papers Status: R It may interest the network to see some of the past papers that have been published in the journal with disks. This is from the cover of the journal. More detailed contents can be obtained by SENDME CONTENTS.V3* sent to fileserv@tcm.ucsc.edu. The TCM style guides and instructions for authors are also available from the fileserver by LIST INSTR and then request the files wanted by SENDME. --------------------------------------------------------------------------- Tetrahedron Computer Methodology 1990 Volume 3, Number 1 Symposium-in-Print No. 1 Three-Dimensional Structure Perception S. Sasaki, Guest Editor S. Sasaki 1 Introduction Tamio Yasukawa, 3 A Method to Detect Common Features Toshimasa Ishida, Necessary for Biological Activity: Shigeyuki Sumiya, Applications of ANALOGS for Aldose Reductase Kunihiro Kitamura Inhibitors Yvonne C. Martin 15 Computer Design of Potentially Bioactive Molecules by Geometric Searching with Aladdin Y. Takahashi, T. Akagi, 27 Three-Dimensional Pharmacophoric Pattern S. Sasaki Searching Using COMPASS: Nootropic Agents J. Cringean, 37 Selection of Screens for Three-Dimensional C. Pepperrell, Substructure Searching A. Poirrette, P. Willett Mathew Clark, 47 Comparative Molecular Field Analysis (CoMFA) 2. Richard D. Cramer III, Toward Its use with 3D-Structural Databases Dumont M. Jones, David E. Patterson, Perrry E. Simeroth 61 Instructions to authors Contents of Disks 1 and 2 Disk 1: CONTENTS.ASC describes each file in detail; *.ASC, ASCII text files of (R) each paper named after an author; TAK.DOC is the ChemText document file for the paper by Takahashi. SCREEN subdirectory: SCREEN.EXE is the IBM-PC executable program that (R) is part of Willett's paper; SCREEN.PAS is the Turbo Pascal source code; ANGLES.DAT is a sample input file and ANGLES.RES is the sample output results; READ.ME describes operation. (R) Disk 2: Macintosh format contains CONTENTS.ASC, the complete contents of all disks in this issue; *.ASC, the ASCII version of all papers; *.MSW (R) are Microsoft Word document files from which the corresponding papers were printed. SCREEN folder: See SCREEN subdirectory above. The IBM-PC executable SCREEN.EXE is not included. --------------------------------------------------------------------------- Tetrahedron Computer Methodology 1990 Volume 3, Number 2 Editorial 61 Introducing Undergraduates to Computer Chemistry Allan Wissner 63 HMO Version 1.1: A Huckel Molecular Orbital Program for the Macintosh Allan Wissner 73 QS-Edit 1.0: A Query Structure Editor for the Macintosh for Use with the CAS Online Registry and Beilstein Databases W. Todd Wipke and 83 An Alternative View of Reaction Similarity: George Vladutz Citation Analysis. Bruno Bienfait 109 A Very Fast Program for ESR Spectrum Simulation Carlos M. Cerda-Garcia-Rojas, 113 A PC Program for Calculation of Dihedral L. Gerardo Zepeda, and Angles from 1H NMR Data Pedro Joseph-Nathan Instructions for Authors Contents of Disks 3 to 6 Disk 3: CONTENTS.ASC contents and descriptions of all files on disks 3-6; EDITOR.ASC, editorial; *.asc, ASCII files of papers in this issue; CHEMTEXT.ARC, ChemText document files for Nathan and Wipke papers compressed in archive. Disk 4 *.ARC, compressed source and executable files for Bienfait's ESR program; INSTALL.BAT, file to install and unpack the ESR program and manuals. Disk 5 RXCITE subdirectory: data files for Wipke and Vladutz paper, see READ.ME for detailed description. ALTONA subdirectory; source code and executable program for Nathan NMR paper. Disk 6: Macintosh format contains CONTENTS.ASC, the complete contents of all disks in this issue; *.MSW, Microsoft Word document files for papers in this issue; *.ASC, the ASCII version of all papers; LORENTZ.C, source code for one of Bienfait's programs for ESR HMO 1.1 folder: Wissner HMO program for Macintosh HMO data folder: Data for HMO 1.1 program QS-Edit 1.0 folder: Wissner query program for CAS and Beilstein Structure folder: Templates used by QS-Edit 1.0 ------------------------------------------------------------------------- Tetrahedron Computer Methodology 1990 Volume 3, Number 3-4 Symposia-in-Print No. 2 NEURAL NETWORKS Guest Editor: Mark E. Lacy Table of Contents HARDCOPY -------- Mark E. Lacy 119 Neural network technology and its application in chemical research Joseph D. Bryngelson, J. J. Hopfield, 129 A protein structure predictor and Samuel N. Southard, Jr. based on an energy model with learned parameters Hudson H. Luce and Rakesh Govind 143 Neural network applications in synthetic organic chemistry: I. A hybrid system which performs retrosynthetic analysis. David W. Elrod, Gerald M. Maggigora, 163 Applications for neural networks and Robert G. Trenary in chemistry. 2. A general connectivity representation for the prediction of regiochemistry. Mark S. Friedrichs and 175 Molecular dynamics of associative Peter G. Wolynes memory hamiltonians for protein tertiary structure recognition George L. Wilcox, Marius Poliac, 191 Neural network analysis of and Michael N. Liebman protein tertiary structure Bo Curry and David E. Rumelhart 213 MSnet: A neural network which classsifies mass spectra Ole Kirk, Martin Barfoed, and 239 Application of a neural network Fredrik Bjrkling in the optimization of an enzymatic synthesis. Eric G. Suchanek, Ph.D. 245 Software Review: NeuralWare Professional II I Instructions for Authors Contents of Disks 7 to 11 Disk 7: CONTENTS.ASC contains all READ.ME files of all disks describing each file in detail; *.ASC, ASCII text files of each paper. Disk 8 *.DOC files are ChemText document files for the respective papers. Disk 9 BRYNGELS.DOC, ChemText document file of Bryngels paper; KIRK.WP, (R) Word Perfect 5.1 document file for Kirk paper; ACME subdirectory: ACME.ARC, neural net files for Luce and Govind paper compressed in ARC format; NETS.ARC, source code of ACME neural net program of Luce and Govind paper. Disk 10:IBM High Density format contains demonstration of NeuralWorks Professional II, reviewed in this issue by Suchanek. Run NWDEMO.BAT to start the demo. Disk 11:Macintosh format contains CONTENTS.ASC, the complete contents of all disks in this issue; *.ASC, the ASCII version of all papers; LUCE.MSW, Microsoft Word format of Luce paper; ACME.sit, contents of ACME subdirectory of Disk 9 (data files and ACME program source program) from Luce and Govind paper in Stuffit archive format. ------------------------------------------------------------------------- Tetrahedron Computer Methodology 1990 Volume 3, Number 5 Table of Contents HARDCOPY -------- Alan R. Katritzky, Miroslaw Szafran, Aromaticity as a Quantitative Concept N. Malhotra, Sana Ullah Chaudry and Part V: A Comparison of Semi-empirical Ernst Anders Methods for the Calculation of Molecular Geometries of Heteroaromatic Compounds and Application of the AM1 and MNDO Methods to the Calculation of Bird's Aromaticity Indices John Paolini, Philip M. Weintraub, Conformationally Restricted Leukotriene Jeffrey S. Sabol, David A. Demeter Antagonists. Modeling and Assignment and H. J. R. Weintraub of Structure of [(Octahydro-2-oxo-7- tetra-decylidene-2H-1-benzopyran-8-yl) thio]acetic Acids Raul E. Valdes-Perez Symbolic Computing on Reaction Pathways Berthold J. Maier A Language for Acyclic Groups Andrea M. Marconi, Noemi Proietti, Computer Aided Nomenclature: The and Errico Zeuli MARK Algorithm for Organic Chemistry Contents of Disks 12 to 15 Disk 12:(IBM 360 kbyte format) CONTENTS.ASC contains all READ.ME files of all disks describing each file in detail; EDITOR.ASC, editorial; *.ASC, ASCII text files of each paper. AUTHORS subdirectory: REFFORM.COM ver 1.1, reference formatting system revision; *.MCR, ChemText macros used with REFFORM; TCMFORMA.WP5, Word Perfect 5.1 style; (R) WORDPERF.ASC, Word Perfect instructions; TCMMSW.RTF, Microsoft Word (R) and Word for Windows style in Rich Text Format; INSTMSW.TXT, instructions for Word style; INSTR.PT1 and INSTR.PT2, instructions for authors; READ.ME, instructions for REFFORM. UTIL subdirectory: (tm MDLTOACR.EXE, ver 2.0, PC program to convert MDL MolFile to AcroSpin format, updated by Gary Anderson; C60.MOL, buckminsterfullerene (tm) structure computed by PRXBLD and MMP2 as an MDL MolFile ; C60OS.MOL, Joel Hawkins x-ray structure of C60 osmium derivative as MolFile; README.TXT, details about MDLTOACR. Disk 13 *.DOC files are ChemText document files for the respective papers; *.MSS, TCM ASCII format of respective paper; *.BIB, bibliography data base of respective paper for BibTeX/REFFORM; VALDES.TEX, LaTeX format of Valdes paper. TEX subdirectory: TCM.STY, TCM DocumentStyle for (tm} LaTeX ; TCM.BST, TCM BibliographyStyle for LaTeX/BibTeX; TIMES.STY, DocumentStyle for Times-Roman font in LaTeX; PSFONTS.MAP, font names required by TIMES.STY. Disk 14 MECHEM.LSP, sample LISP code from Valdes paper; ALKANES subdirectory: ALKANES.EXE, PC executable program for nomenclature by Zeuli; ALKANES.TXT, user manual for the ALKANES program. SCREEN subdirectory: Erratum update of Willett's SCREEN program previously published, SCREEN.EXE, new corrected executable. MAIER subdirectory: Pascal source code and PC executable code for Maier acyclic language parser; LP.PAS, main program; LSF.PAS, syntax analyser; SCAN.PAS, parser; *.INT, interfaces; SAMPLE.IN, formulas in section 4 of paper; SAMPLE.OUT, output of the parser for SAMPLE.IN; LP.EXE, PC executable code. Disk 15:Macintosh format contains CONTENTS.ASC, the complete contents of all disks in this issue; *.ASC, the ASCII version of all papers; paolini.msw, Microsoft Word format, Paolini paper; *.BIB, bibliography data base for respective paper in BibTeX or REFFORM format; C60.MOL, buckminsterfullerene structure computed by PRXBLD and MMP2 as MolFile; C60OS.MOL, Joel Hawkins x-ray structure of C60 osmium derivative as MolFile; VALDES.TEX, LaTeX format of Valdes paper (ASCII text); VALDES.BIB, BibTeX bibliography data base for Valdes paper; QS-Edit 1.02, update of Wissner's program published in Vol 3, No 2 to correct error. authors folder: INSTR.PT1 and INSTR.PT2, instructions for authors pt 1 and 2 (ASCII text); TCMformat.msw, Microsoft Word style and skeleton compuscript; INSTMSW.TXT, instructions for using TCMformat.msw. (Last published on Macintosh disk in Vol 2, no 1.) Maier folder: Pascal source code and input and output files for Maier's acyclic language parser (see Disk 14 MAIER above), PC executable not included on Macintosh disk. paolini folder: X-rayData, report of x-ray determination. TeX folder: style files for LaTeX/BibTeX typesetting system, see Dsk 13 TeX subdirectory above for contents and description. Macintosh is a trademark of Apple Computer Co. ChemText and MolFile are trademarks of Molecular Design Limited, San Leandro, CA. Word Perfect is a trademark of Word Perfect Corporation. Microsoft Word and Word for Windows are trademarks of Microsoft Corporation, Seattle, WA. TeX is a trademark of the American Mathematical Society. AcroSpin is a trademark of Acrobits, Salt Lake City, UT. Note: Computers that can not read IBM or Mac format disks can download files from TCM-Online: fileserv@TCM.ucsc.edu or via the TCM-Online BBS, (408) 429-8019. -----------------------------------------------------------------------------