From chemistry-request@ccl.net Mon May 4 00:52:06 1992 Date: Sun, 03 May 1992 19:22:26 PDT From: "W. Todd Wipke" Subject: Volume 3 Number 6B in press To: tcm-online@SECS.UCSC.EDU Status: RO Tetrahedron Computer Methodology 1990 Volume 3, Number 6b HARDCOPY -------- Contributors to this issue Editorial The Golden Age of Computational Chem. Sergio Clementi, Gabriele Cruciani, Chemometric Approach to a QSAR Study of Daniela Riganelli, Paolo Rovero, Peptides Behaving as NK-2 Receptor Vittorio Pestellini, Antagonists Carlo Alberto Maggi, and Massimo Baroni Ekaterina V. Gordeeva, General Methodology and Computer Program Marina S. Molchanova, and for the Exhaustive Restoring of Chemical Nicolai S. Zefirov Structures by Molecular Connectivity Indexes. Solution of the Inverse Problem in QSAR/QSPR Dmitri E. Lushnikov, Search for the Bullvalene-Like Ekaterina V. Gordeeva, and Structures Nickolai S. Zefirov Ekaterina V. Gordeeva, The ICAR Program: Computer-Assisted Vladimir V. Shcherbukhin, and Investigation of Carbocationic Nikolai S. Zefirov Rearrangements Ekaterina V. Gordeeva, COMPASS Program: Combination of Empiri- Dmiitri E. Lushnikov, and cal Rules and Combinatorial Methods for Nikolai S. Zefirov Planning of Organic Synthesis F. Haase and K. Biedka Heterocyclic Reaction Design with RDSS Eric Fontain The Generation of Reaction Networks with RAIN. 2. Resonance Structures and Tautomerism Xu Jun, B. N. Gray, and L. R. Brown Branched Trees and Coherence Transfer Pathways in Multi-Dimensional NMR Spectroscopy: Use of the HBA Algorithm to Predict Spectra M. R. Whitbeck Numerical Modeling of Chemical Reaction Mechanisms Andrew C. Regan and Alan A. Smith MMOL: A Utility for Importing MacroModel Structure Files into ChemText Stephen R. Wilson and Harikila Dris Extraction of 3-Dimensional Coordinates from a Stereo Picture Tamas E. Gunda MOLCONV: A Powerful Interface Program for Converting Molecule Structure Files Between PC Based Modeling Programs Software Reviews Gary Anderson PLT V5.0 Gary Anderson ChemWords 1.1 Instructions for Authors DISKS 16-18 ------------ Disk 19 ASCII text files of the papers Directory of Disk TCMV3N6B D19 IBM format (360 K byte) CONTENTS ASC 4679 04-15-92 5:45p Contents of all disks (this file) EDITORIA ASC 4003 12-20-91 3:30p Editorial by Wipke ANDERS2 ASC 5138 04-24-92 12:33a Software Review PLT V5.0 ANDERSON ASC 3201 07-30-91 3:24p Software Review ChemWords 1.1 BIEDKA ASC 18678 04-24-92 12:04a Heterocyclic Reaction Design BROWN ASC 40666 04-24-92 12:10a Branched Trees ... NMR CLEMENTI ASC 31467 03-25-92 11:54p QSAR study of Peptides FONTAIN ASC 24005 07-01-91 1:43p RAIN 2. Resonance structures GUNDA ASC 23357 08-01-91 9:56a Molconv: converting structure files SMITH ASC 6050 04-24-92 12:12a MMOL: Utility for importing MacroModel WILSON ASC 8309 04-24-92 12:06a Coordinates from Stereo Pictures ZEFIROV1 ASC 21893 09-05-91 12:00p Bullvalene structures ZEFIROV2 ASC 57339 09-12-91 2:56p Structures from Connectivity Indices ZEFIROV3 ASC 34994 09-05-91 11:13a ICAR program: Carbocations ZEFIROV4 ASC 36048 09-05-91 9:50a COMPASS program: Organic Synthesis ======================================================================== Disk 20 Document wordprocessor files Directory of TCMV3N6B D20 IBM PC 360 Kbyte format ANDERS2 RTF 7156 04-25-92 3:48p Software Review PLT V5.0 BIEDKA DOC 53248 04-22-92 8:34p Heterocyclic Reaction Design BROWN RTF 115338 09-18-91 3:17p Branched Trees ... NMR CLEMENTI RTF 42999 07-18-91 10:31a QSAR study of Peptides CONVG TEX 34658 04-22-92 11:23p Required for Whitbeck FONTAIN RTF 24266 03-26-92 12:19a RAIN 2. Resonance structures GUNDA DOC 65536 08-01-91 9:29a Molconv: converting structure files MODEL0 TEX 16018 04-22-92 11:23p Required for Whitbeck MODEL1 TEX 20498 04-22-92 11:23p Required for Whitbeck PROGRAM STY 4242 04-22-92 11:23p Required for Whitbeck (program listing SMITH DOC 28672 04-22-92 8:21p MMOL: Utility for importing MacroModel WHITBECK TEX 22326 04-25-92 2:37p Paper on REACT program WILSON RTF 58470 04-25-92 2:56p Coordinates from Stereo Pictures ZEFIROV1 DOC 102400 09-05-91 12:11p Bullvalene structures ZEFIROV2 DOC 303104 09-12-91 2:38p Structures from Connectivity Indices ZEFIROV3 DOC 143360 09-05-91 11:03a ICAR program: Carbocations ZEFIROV4 DOC 122880 09-05-91 9:28a COMPASS program: Organic Synthesis These are document files to be viewed by word processors. The RTF files can be read by MS Word, and Word for Windows on the PC. The MSS file can be printed by SCRIBE, SPRINT, Final Word and is the TCM ASCII mark-up language. WHITBECK.TEX is LaTeX and requires the other *.TEX files as included files (a large memory is needed for this particular LaTeX document, EMTEX on the PC can't handle it. The DOC files are Molecular Design Limited ChemText document files. NOTE: The printed copy was made from these files, there is nothing in these files that is not present in the printed copy. ======================================================================== Disk 21 Program files Directory of TCMV3N6B D21 IBM PC 1.2 Megabyte format MOLCONV 04-25-92 3:04p Program from Gunda paper MMOL 04-25-92 3:05p Program from Regan and Smith paper COMPAS 04-25-92 3:06p Program from Zefirov COMPASS paper ICAR 04-25-92 3:06p Program from Zefirov ICAR paper RVD DAT 1024 06-06-91 10:50a Data file from Clementi paper DEMORING EXE 54591 05-29-90 6:45p Program for Zefirov QSAR/QSPR paper 3D FOR 12152 04-22-92 3:18p Program from Wilson Paper SubDirectory A:\ICAR RUNME EXE 290593 10-30-90 4:36p READ ME 1810 04-25-92 3:14p RUNME.EXE c:\icar will unpack the files for ICAR into the icar directory on C: giving you the following files: Searching ZIP: a:RUNME.EXE Length Method Size Ratio Date Time CRC-32 Attr Name ------ ------ ----- ----- ---- ---- ------ ---- ---- 13362 Implode 5292 61% 10-05-90 18:37 d84c8389 --w MANUAL.ASC 11960 Implode 8261 31% 10-22-90 13:18 80d090a3 --w ICARUS.COM 5716 Implode 3902 32% 01-30-90 16:23 e871162a --w ICAR.CGA 11646 Implode 8001 32% 10-22-90 13:18 7342c700 --w SETUP.COM 35020 Implode 11361 68% 09-12-90 19:58 c4515cd5 --w ICAR.EGA 71543 Implode 39340 46% 10-01-90 15:35 064e654b --w _SETUP.EXE 252304 Implode 112226 56% 10-25-90 20:49 178e7d18 --w ICAR.EXE 16084 Implode 5295 68% 10-11-90 17:47 4249c4d5 --w ICAR.HLP 88833 Implode 50244 44% 08-04-87 12:05 ee5c2a5f --w METAWNDO.EXE 982 Implode 285 71% 01-19-90 12:56 930f80fa --w ICAR.FLB 2276 Implode 1170 49% 09-27-85 00:33 ee3892f7 --w ICAR.FNT 9185 Implode 5562 40% 01-31-90 14:53 1eb5318a --w ICAR.HER 1138 Implode 500 57% 03-21-90 14:19 da70cf7e --w ICAR.KBS 617 Implode 288 54% 06-16-90 21:20 5e46e2d0 --w NORB.KBS 269 Shrunk 213 21% 01-04-90 18:12 6517ebdb --w ADAMANT.STR 104 Shrunk 79 25% 12-29-89 19:15 c01ef5f3 --w NORB.STR 77675 Implode 20646 74% 07-22-90 16:29 92a5dccb --w ADAMANT.TRE 11314 Implode 3432 70% 07-22-90 16:33 24656435 --w NORB.TRE ------ ------ --- ------- 610028 276097 55% 18 Read the paper about ICAR in this issue and the MANUAL.ASC for operating instructions. COMPAS Subdirectory DOCOMPAS EXE 359794 11-28-90 1:46p Self extracting zip file READ ME 4743 04-25-92 3:23p How to install the COMPASS program COMPAS LIS 1546 04-25-92 1:33p List of files in the zip READ.ME - how to install COMPASS program System requirements. The program requires 750 Kbyte of disk space and 450-500 Kbyte of RAM. Please check the size of free memory before execution of the program by means of DOS comand CHKDSK. If memory is insufficient please remove some resident programs from AUTOEXEC.BAT or CONFIG.SYS files (except mouse driver !) and reboot the system. Warning : otherwise the program may crash at any time !. The program can operate on the various graphics boards due to METAWINDOW graphics driver (licensed program material of Metagraphics Software Corporation. Copyright (c) 1986,1987 Metagraphics Software Corporation, Scotts Valley, CA 95066). The full list of supported graphics devices is shown during installation procedure. The authors have checked the program action on IBM CGA, EGA, VGA, and Hercules graphics adaptors. Installation procedure. To install the COMPASS program 750 KB hard disk space is required. a) Make subdirectory for COMPAS program (for example C:\COMPASS ) b) Insert program diskette into drive a: and type under DOS prompt DOCOMPAS C:\COMPASS (drive and subdirectory to install program) After successful installation procedure You will have the next files in the subdirectory : INSTALL EXE - this file makes compas.bat (file to start the program) INST EXE - installation program COMPAS BAT - batch file to run program COMPASS CFG - COMPASS configuration file COMPASS DBA - knowledge base COMP EXE - COMPASS program file COMPRUN EXE - file to execute comp.exe COMPASS HLP - help file READ ME - instructions how to start the program METAWNDO EXE - graphics driver COMPASS DEM - key sequences for demo-mode * CMP - files with target structures * TRE - files with synthetic trees TITLE EXE - indication of the title on the EGA/VGA graphics screen TITLE TIT - picture with title of the program PROLOG ERR - Turbo Prolog error file c) Change directory to COMPASS drive and subdirectory and type INSTALL under DOS prompt Select DEFAULT mouse and DEFAULT adaptor. DEFAULT selection of adaptor and mouse turn the program to recognize type of them automatically. If the automatic procedure fails, then try to install type of adaptor and mouse by selection of appropriate option in menu. If You see after installation black screen, cheer up ! It means that ANSI.SYS driver isn't included in You CONFIG.SYS file. Then type CLS, press ENTER and the appropriate DOS prompt will be shown on the screen. Running the program To begin program type under DOS prompt COMPAS To begin demonstration mode type COMPAS DEMO Non-empirical part of the program is implementation of the FLAMINGOES program. Brief explanations concerning menus and options You may get by pressing F1 - help key where it is needed. Another way is to print help file COMPASS.HLP. Another way is to print MANUAL.TXT. The zipped DOCOMPAS.EXE file listing is: Searching ZIP: a:DOCOMPAS.EXE Length Method Size Ratio Date Time CRC-32 Attr Name ------ ------ ----- ----- ---- ---- ------ ---- ---- 22 Stored 22 0% 01-17-90 16:49 a952425a --w COMPAS.BAT 2590 Implode 1153 56% 11-13-90 15:36 f55ed3fb --w COMPASS.CFG 7617 Implode 1497 81% 09-27-90 14:20 a19896dd --w COMPASS.DBA 9578 Implode 601 94% 10-25-90 18:22 0de7807a --w COMPASS.DEM 33438 Implode 10595 69% 06-21-88 02:00 d5766313 --w PROLOG.ERR 346256 Implode 163989 53% 11-13-90 15:27 6bfeaac4 --w COMP.EXE 16608 Implode 10055 40% 12-20-89 17:09 bba0f1d2 --w COMPRUN.EXE 88755 Implode 51027 43% 11-13-90 15:31 617b70ad --w INST.EXE 16848 Implode 10073 41% 11-13-90 15:31 ba109d0d --w INSTALL.EXE 88833 Implode 50244 44% 08-04-87 12:05 ee5c2a5f --w METAWNDO.EXE 29086 Implode 16529 44% 01-17-90 15:33 91b3ed06 --w TITLE.EXE 17103 Implode 5439 69% 11-13-90 15:39 2b666335 --w COMPASS.HLP 55021 Implode 18338 67% 11-16-89 14:26 cafd8cc4 --w TITLE.TIT 18578 Implode 5984 68% 11-28-90 12:44 58e50efe --w MANUAL.TXT 2 Stored 2 0% 11-28-90 13:45 14a285ac --w DEMO.TRE ------ ------ --- ------- 730335 345548 53% 15 Directory of A:\MMOL MMOL FOR 10273 09-27-90 10:06a Source of Regan and Smith READ ME 2052 04-24-92 12:55a Instructions VAXMMOL EXE 7680 09-27-90 10:30a Code to run on vax (binary) MMOL EXE 135964 11-06-90 9:19a Code to run on PC (binary) These files are part of the paper Andrew C. Regan and Alan A. Smith, "MMOL: A Utility for Importing MacroModel Structure files into ChemText". Tetrahedron Computer Methodology, 1990, 3, 6b, disk D20 MMOL.EXE is for the PC VAXMMOL.EXE is for the vax MMOL.FOR is source code minus Molecular Design MolFile format statements because MDL holds the MolFile format proprietary. DO NOT TRY TO RUN VAXMMOL ON THE PC, IT WILL HANG FORCING REBOOT!!!!!!!!!! We have found that when Kermit transferes a FORTRAN output file the initial code in the record is changed. This results in an extra line being added to the file. Thus the MolFile written be MMOL.EXE has two blank lines at it's beginning. Kermit will add one line to gile the required three lines. It is possible that other users transfer their text files using a different method (eg. EMU-TEK Capture File). In this case three blank lines will be required. We have supplied a second version MMOL3.EXE which does generate the correct initial three blank line MolFile format. _______________________________________________________________________________ Note: When the file VAXMMOL.EXE is transfered to the VAX the VAX KERMIT programme must be told that the the incomming file is of fixed record length. Issue the following to Kermit-32... Kermit-32> set file type fixed I have transferred VAXMMOL.EXE at 9600 baud without any problems. _______________________________________________________________________________ If one wishes to run the program on a Silicon Graphics Work Station then the missing FORMAT statements will have to be found. This will be trivial and may easily be done by inspecting the code and a MolFile or two! An important point: If the code is recompiled you must ensure that the compiler writes out real number (-1