From thomas@salz.phych.ba-freiberg.de Tue Jul 26 04:57:02 1994 Received: from salz.phych.ba-freiberg.de for thomas@salz.phych.ba-freiberg.de by www.ccl.net (8.6.9/930601.1506) id EAA13645; Tue, 26 Jul 1994 04:56:12 -0400 From: Received: by salz.phych.ba-freiberg.de (AIX 3.2/UCB 5.64/4.03) id AA13756; Tue, 26 Jul 1994 10:57:30 +0200 Message-Id: <9407260857.AA13756@salz.phych.ba-freiberg.de> Subject: Summary - 3D programs To: chemistry@ccl.net Date: Tue, 26 Jul 94 10:57:29 DFT X-Mailer: ELM [version 2.3 PL2] In the last week i asked for a public domain program which can handle 3D-plots ============================================================================== As a result of my request i've got a lot of messages. Most people has recommended "gnuplot". Here are some messages: ------------------------------------------------------------------------------- " ++++++++++++++++++++++ 3D Plotting Packages ++++++++++++++++++++++++++++++++++++ Gnuplot 3.5 It is one of the best 2- and 3-D plotting packages, with online help. It's a command-line driven interactive function plotting utility for UNIX, MSDOS, Amiga, Archimedes, and VMS platforms (at least!). You can practically find it everywhere (use Archie to find a site near you!). Robot Release 0.48 : 2-D and limited 3-D. Based on XView 3, written in C / Fortran (so you need a Fortran compiler or the f2c translator). Mainly tested on Sun4, less on DECstations. Check at ftp.astro.psu.edu (128.118.147.28), pub/astrod. PlotMTV tanqueray.berkeley.edu : /pub/Plotmtv1.3.1.tar.Z (~1 MB) - with source The program can do 2D and 3D line/scatter plots, vector plots, as well as contour plots. Contours can be plotted from regular rectangular meshes, triangular meshes, as well as random data. " ------------------------------------------------------------------------------- - contour ------------------------------------------------------------------------------- " There is program called contour which can create 2d countour plots. I think you can get it from : Host ftp.denet.dk (129.142.6.74) Last updated 14:24 20 Jul 1994 Location: /mirror2/X11/R5contrib FILE -r--r--r-- 144942 bytes 04:00 12 Jun 1992 contour.tar.Z " ------------------------------------------------------------------------------- - SciAn and Khoros ------------------------------------------------------------------------------- " If you need the fancy stuff, my best guess for public domain programs are Scian, but it used to run only on SGI or IBM with 3d graphics and z-buffer, or Khoros, which runs under X-window, it is less sophisticated than Scian in terms of screen output quality, and it is a bit difficult to install. but there are mailing lists and users group on the net devoted to khoros. SciAn used to be distributed via anonymous ftp from ftp.scri.fsu.edu The best way to find the latest version of Khoros is to search on the network using Archie, Veronica or mosaic. " ------------------------------------------------------------------------------- - Molgen (but MS-DOS !?) ------------------------------------------------------------------------------- " Try Molgen, on ccl.net, /pub/chemistry/software/MS-DOS/MOLGEN-demo. " ------------------------------------------------------------------------------- - pdraw ------------------------------------------------------------------------------- My opinion: pdraw can handle X-Y-Z-plots as points or lines. The output goes to screen (X-Window) or/and to a Postscript-Printer. A problem is the description of the axis and the legends with others than the standard-font (greek, symbols etc.). ------------------------------------------------------------------------------- - another program : ------------------------------------------------------------------------------- " We have developed a package for such a visualization. It plots a quantity as a texture on a molecular surface or provides a chickenwire (stack-contour) plot or a dot surface. Please supply more details of what and how you like to visualize. Professor Shridhar Gadre Department of Chemistry University of Poona Pune-411007. INDIA. " ------------------------------------------------------------------------------- Thank you for the helpfull informations !! thomas@salz.phych.ba-freiberg.de From young@semi.korea.ac.kr Tue Jul 26 09:56:38 1994 Received: from han.hana.nm.kr for young@semi.korea.ac.kr by www.ccl.net (8.6.9/930601.1506) id JAA16025; Tue, 26 Jul 1994 09:54:22 -0400 Received: from kuccgx.korea.ac.kr by han.hana.nm.kr (4.1/KUM-0.1) id AA04063; Tue, 26 Jul 94 21:25:37 KST Received: from semi.korea.ac.kr by kuccgx.korea.ac.kr (AIX 3.2/UCB 5.64/4.03) id AA06942; Tue, 26 Jul 1994 22:03:06 -1500 Received: by semi.korea.ac.kr (4.1/SMI-4.1) id AA00813; Tue, 26 Jul 94 22:32:34 KDT From: young@semi.korea.ac.kr (Hyun Su Kim) Message-Id: <9407261232.AA00813@semi.korea.ac.kr> Subject: change my e-mail address.. To: chemistry@ccl.net Date: Tue, 26 Jul 94 22:32:33 GMT+9:00 X-Mailer: ELM [version 2.4dev PL32] Dear Netters, I have to change my e-mail address to young@semi.korea.ac.kr Please contact me, if you wanna send a message. Korea University Chemistry Department Physical Chemistry... young@semi.korea.ac.kr From srheller@asrr.arsusda.gov Tue Jul 26 10:01:03 1994 Received: from asrr.arsusda.gov for srheller@asrr.arsusda.gov by www.ccl.net (8.6.9/930601.1506) id JAA15727; Tue, 26 Jul 1994 09:29:40 -0400 Message-Id: <199407261329.JAA15727@www.ccl.net> Date: 26 Jul 94 09:19:00 EDT From: "STEPHEN R. HELLER" Subject: More Software/Databases for Review To: "chemed-l" cc: "chminf-l" , "chemistry" , "orgchem" 26 July, 1994 Subject: Computer Software for Review As the Software Review Editor for the ACS Journal of Chemical Information and Computer Science (JCICS) I often get software for review in the journal. Since I sent a note out yesterday two additional packages have arrived. I am looking for someone who is willing to review these software/databases products. In return for the review you get to keep the software. The review should be completed in 1-3 months. The length of the review is 4-10 double spaced typed pages. Sample reviews can be found in most of the recent issues of JCICS. Please try to give me some (short) reason to choose you over another person. DO NOT SAY YOU WILL REVIEW ANYTHING I HAVE AVAILABLE. Messages with such replies are trashed! I have tried this approach for about the past three years and it is working reasonably well. (REMINDER: For those who haven't finished your reviews of software sent months and months ago, this last sentence does not apply to you!) As a result, I am continuing this new method to find reviewers using this e- mail/user group system. I reserve the right to abandon this if it is a problem, or inappropriate. I will not notify people if I have found a reviewer. If you don't hear from me within a few days I have chosen someone else to review the particular package. As I get many, many, (too many) replies to this message, please do not respond after 27 July, 1994 (Wednesday), as I am sure the software will be gone by then. I can be reached on Internet (SRHELLER@ASRR.ARSUSDA.GOV). PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE, and FAX NUMBER!!! (I send the software by Federal Express.) Without this information I WILL NOT consider your request. Steve Heller The two additional packages I now have are from Megalon: 1. ChemStructure for Windows. It is a structure drawing program. 2. Compounds for Windows. A database of about 27,000 organic compounds with some two dozen types of numeric and spectral data associated with each compound. From E.A.Wilinska@open.ac.uk Tue Jul 26 11:56:46 1994 Received: from venus.open.ac.uk for E.A.Wilinska@open.ac.uk by www.ccl.net (8.6.9/930601.1506) id LAA17337; Tue, 26 Jul 1994 11:18:55 -0400 Message-Id: <199407261518.LAA17337@www.ccl.net> Received: from acsvax.open.ac.uk by venus.open.ac.uk with Mail-11 (PP) id <02306-0@venus.open.ac.uk>; Tue, 26 Jul 1994 16:18:10 +0100 Date: Tue, 26 Jul 1994 16:18:10 +0100 From: Elzbieta Wilinska To: chemistry@ccl.net X-VMS-To: MAIL1::"chemistry@ccl.net" Cc: E.A.Wilinska@open.ac.uk X-VMS-Cc: EA_WILINSKA Subject: pK values for methylated lysin. Hello, Does anyone know where to find the pK values for methylated derivatives of lysin: mono-N-epsilon-methyllysin, di-N-epsilon-methyllysin, tri-N-epsilon-methyllysin? Or how to calculate them? ---------------------------------------------------------------------------- Ela Wilinska ea_wilinska@uk.ac.open Oxford Research Unit tel.0865 328178 The Open University fax 0865 326322 Berkeley Rd. Oxford OX1 5HR ---------------------------------------------------------------------------- From schw0531@compszrz.zrz.tu-berlin.de Tue Jul 26 12:56:38 1994 Received: from mailgzrz.TU-Berlin.DE for schw0531@compszrz.zrz.tu-berlin.de by www.ccl.net (8.6.9/930601.1506) id MAA18480; Tue, 26 Jul 1994 12:37:42 -0400 Received: from compszrz.zrz.TU-Berlin.DE by mailgzrz.TU-Berlin.DE (5.65c/ZRZ-MX) for id AA02392; Tue, 26 Jul 1994 18:38:06 +0200 Date: Tue, 26 Jul 94 18:38:05 +0200 From: Helmut Schwarz Message-Id: <9407261638.AA14651@compszrz.zrz.tu-berlin.de> To: chemistry@ccl.net Subject: Gaussian geometry opt Hi Gaussian world, Couls somebody help me with a problem in Gaussian Fletcher-Powell geometry optimization? For some procedures analytical gradients are not available in the Gaussian code. Often when using FP algorithm the Error message FPERR ACTIVE: -1 1.8112400 1.8301373 0.18897260e-01 0.00000000e+00 0.30647650e-02 -91 .500004 0.00000000e+00 0.00000000e+00 2.0210047 2.0210047 0.18897260e-01 0.00000000e+00 0.00000000e+00 0.0 0000000e+00 0.00000000e+00 0.00000000e+00 2.7177144 2.7177144 0.18897260e-01 0.00000000e+00 0.00000000e+00 0.0 0000000e+00 0.00000000e+00 0.00000000e+00 1.7910862 1.7910862 0.17453293e-01 0.00000 .....etc. appeares. How to avoid this problem ? Jan Hrusak TU Berlin schw0531@compszrz.zrz.tu-berlin.de From schw0531@compszrz.zrz.tu-berlin.de Tue Jul 26 14:56:39 1994 Received: from mailgzrz.TU-Berlin.DE for schw0531@compszrz.zrz.tu-berlin.de by www.ccl.net (8.6.9/930601.1506) id OAA19752; Tue, 26 Jul 1994 14:08:57 -0400 Received: from compszrz.zrz.TU-Berlin.DE by mailgzrz.TU-Berlin.DE (5.65c/ZRZ-MX) for id AA04380; Tue, 26 Jul 1994 20:08:02 +0200 Date: Tue, 26 Jul 94 20:08:01 +0200 From: Helmut Schwarz Message-Id: <9407261808.AA16881@compszrz.zrz.tu-berlin.de> To: chemistry@ccl.net Subject: Gaussian geometry opt Hi Gaussian world, I still have problems with the gaussian geometry optimization procedures. By using the GAUSSIAN92/DFT program with the input : #N becke3lyp/6-31G** opt=calcall scfcyc=300 IOP(2/16=1) optcyc=100 scf=(direct,nosave,qc) int=finegrid I sometimes after few gradient cycles obtained the following Item Value Threshold Converged? Maximum Force .003549 .000450 NO RMS Force .001786 .000300 NO Maximum Displacement .198078 .001800 NO RMS Displacement .074918 .001200 NO Predicted change in Energy=-2.551447D-05 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad ------------------------------------------------------------------------ Z-MATRIX (ANGSTROMS AND DEGREES) CD Cent Atom N1 Length/X N2 Alpha/Y N3 Beta/Z J ------------------------------------------------------------------------ 1 1 H 2 2 C 1 3.111513( 1) 3 3 O 2 1.284844( 2) 1 90.112( 8) 4 4 O 2 1.284844( 3) 1 90.112( 9) 3 120.004( 14) 0 5 5 O 2 1.284844( 4) 1 90.112( 10) 3 -120.004( 15) 0 6 6 H 3 .978405( 5) 2 113.719( 11) 1 270.235( 16) 0 7 7 H 4 .978405( 6) 2 113.719( 12) 1 270.235( 17) 0 8 8 H 5 .978405( 7) 2 113.719( 13) 1 270.235( 18) 0 ------------------------------------------------------------------------ Z-Matrix orientation: ---------------------------------------------------------- ---------------------------------------------------------- Center Atomic Coordinates (Angstroms) Number Number X Y Z ---------------------------------------------------------- 1 1 .000000 .000000 .000000 2 6 .000000 .000000 3.111513 3 8 1.284842 .000000 3.114021 4 8 -.642491 1.112665 3.114021 5 8 -.642491 -1.112665 3.114021 6 1 1.678409 -.895753 3.111115 7 1 -.063579 1.901418 3.111115 8 1 -1.615013 -1.005567 3.111115 ---------------------------------------------------------- Distance matrix (angstroms): 1 2 3 4 5 1 H .000000 2 C 3.111513 .000000 3 O 3.368671 1.284844 .000000 4 O 3.368671 1.284844 2.225452 .000000 5 O 3.368671 1.284844 2.225452 2.225330 .000000 6 H 3.646707 1.902480 .978405 3.069255 2.331016 7 H 3.646707 1.902480 2.331016 .978405 3.069176 8 H 3.646707 1.902480 3.069255 2.330819 .978405 6 7 8 6 H .000000 7 H 3.295252 .000000 8 H 3.295252 3.295073 .000000 Interatomic angles: H1-C2-O3= 90.1119 H1-C2-O4= 90.1119 O3-C2-O4=120.0032 H1-C2-O5= 90.1119 O3-C2-O5=120.0032 O4-C2-O5=119.9924 C2-O3-H6=113.7188 C2-O4-H7=113.7188 C2-O5-H8=113.7188 Symmetry turned off by external request. PREVIOUS ROTATION MATRIX USED. Standard orientation: ---------------------------------------------------------- Center Atomic Coordinates (Angstroms) Number Number X Y Z ---------------------------------------------------------- 1 1 NaNQ NaNQ NaNQ 2 6 NaNQ NaNQ NaNQ 3 8 NaNQ NaNQ NaNQ 4 8 NaNQ NaNQ NaNQ 5 8 NaNQ NaNQ NaNQ 6 1 NaNQ NaNQ NaNQ 7 1 NaNQ NaNQ NaNQ 8 1 NaNQ NaNQ NaNQ ---------------------------------------------------------- Rotational constants (GHZ): NaNQ NaNQ NaNQ Isotopes: H-1,C-12,O-16,O-16,O-16,H-1,H-1,H-1 Standard basis: 6-31G(D,P) (S, S=P, 6D, 7F) Integral buffers will be 262144 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned off. 80 basis functions 140 primitive gaussians 17 alpha electrons 16 beta electrons nuclear repulsion energy NaNQ Hartrees. One-electron integrals computed using PRISM. GenFmT: Coulomb series failed... Error termination in Lnk1e. This occures not only for this particular system but quite often in geometry optimizations by using this program. How one can avoid this error termination? Jan Hrusak TU Berlin schw0531@compszrz.zrz.tu-berlin.de From vaisman@gibbs.oit.unc.edu Tue Jul 26 21:56:46 1994 Received: from gibbs.oit.unc.edu for vaisman@gibbs.oit.unc.edu by www.ccl.net (8.6.9/930601.1506) id VAA23747; Tue, 26 Jul 1994 21:12:16 -0400 Received: from localhost by gibbs.oit.unc.edu (8.6.4.3/10.1) id VAA05875; Tue, 26 Jul 1994 21:13:09 -0400 Date: Tue, 26 Jul 1994 21:13:08 -0400 (EDT) From: Iosif Vaisman Subject: Molecular Modeling Conference 1994 To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Molecular Modeling Conference 1994 Fundamentals and Applications for the Pharmaceutical Industry 2-4 October 1994 Brunswick Hilton and Towers, East Brunswick, New Jersey Molecular Modeling Conference 1994 is organized by Advanstar Communications, the publishers of Pharmaceutical Technology, BioPharm, LC-GC, and Spectroscopy magazines. Conference Moderators: Alexander MacKerell, Assistant Professor, Department of Pharmaceutical Sciences, University of Maryland at Baltimore Alexander Tropsha, Assistant Professor, Director, Laboratory for Molecular Modeling, University of North Carolina at Chapel Hill Herschel J.R. Weintraub, Assistant Director, Medicinal Chemistry, R.W. Johnson Pharmaceutical Research Institute Sunday, 2 October 1994 Afternoon Session: Optional Introductory Workshop - Molecular Modeling Basics Instructors: Warren J. Hehre, Wavefunction, Inc., and University of California, Irvine Alexander Tropsha (Session Organizer), University of North Carolina, Chapel Hill Herschel J.R. Weintraub, R.W. Johnson Pharmaceutical Research Institute Monday, 3 October 1994 Plenary Lecture: Molecular Modeling - For Better, For Worse. For Richer, For Poorer. Peter Goodford, University of Oxford, UK On the Effect of Long-range Interactions on Protein Structure, Specificity, & Ligand Binding Free Energies Arnie Hagler, Biosym Technologies, Inc. Modeling Selectivity in Organic Reactions Warren J. Hehre, Wavefunction, Inc. and University of California, Irvine General Representation and Solution of the QSAR Problem Based Upon Tensor Analysis A. J. Hopfinger, University of Illinois at Chicago Rapid Prediction of Binding Energies Using Continuum Methods Barry Honig, Columbia University Pharmacophore Determination: The Critical Decision in Ligand-Based Design Richard D. Cramer, Tripos, Inc. Overview of 3D-Searching: A Powerful Technique for Computer-Assisted Molecular Design Robert S. Pearlman, University of Texas, Austin Tuesday, 4 October 1994 X-ray Crystallographic Analysis of Macromolecular Structures Wayne A. Hendrickson, Columbia University Free Energy Modeling Monte Pettitt, University of Houston Multidimensional Heteronuclear NMR of Proteins Angela M. Gronenborn, NIDDK, National Institutes of Health Models of G Protein-Linked Receptors: How Do We Get Them and What Can We Do With Them? Charles Hutchins, Abbott Laboratories Comparative Homology Modeling: What Is It Good For and How Well Does It Work? Jonathan Greer, Abbott Laboratories De Novo Predications of Quaternary Protein Structure: Applications to Coiled Coils Jeffrey Skolnick, Scripps Research Institute Computer Assisted Ligand Design I.D. Kuntz, University of California, San Francisco Retrospective and Prospective Successes of Molecular Modeling in the Pharmaceutical Industry Peter Gund, Molecular Simulations Inc. Registration Information To register or to receive a copy of the conference program brochure, please call the Molecular Modeling Conference Registrar at (800) 343-3423 or (503) 343-1200. Fees for Molecular Modeling Conference include all course materials, a copy of the conference proceedings, admission to the Technology Demonstration Room, the Optional Introductory Workshop, and refreshment breaks. Fees Early (postmarked by 19 August 1994): $545.00 Regular (postmarked after 19 August 1994): $645.00 On-Site: $695.00 For more information, contact: Molecular Modeling Conference 1994 859 Willamette Street Eugene, OR 97401-6806 Phone: (800) 343-3423 or (503) 343-1200 Fax: (503) 343-7024 From lim@rani.chem.yale.edu Tue Jul 26 22:58:01 1994 Received: from rani.chem.yale.edu for lim@rani.chem.yale.edu by www.ccl.net (8.6.9/930601.1506) id WAA24490; Tue, 26 Jul 1994 22:48:57 -0400 Received: by rani.chem.yale.edu; Tue, 26 Jul 94 22:44:38 -0400 From: Dongchul Lim Message-Id: <9407270244.AA22092@rani.chem.yale.edu> Subject: Creating input files for PSI88 package from Gaussian Formcheck files To: chemistry@ccl.net (Computational Chemistry) Date: Tue, 26 Jul 94 22:44:36 EDT X-Mailer: ELM [version 2.3 PL11] *************************************************** ***** Update on the PSI88 Package of Programs ***** *************************************************** ____________________________________________________________________________ This post is regarding how to generate input files for PSI88 package >from a Gaussian-related files. I'm posting this message on the request of one of co-authors of PSI88. So this is official almost :-). D. Lim, Department of Chemistry, Yale University. lim@rani.chem.yale.edu ____________________________________________________________________________ 1. What is 'PSI88' and where can I get it? The PSI88 is a MO plotting package, which is written by Prof. William Jorgensen and Dr. Severance at Yale University and available from www.ccl.net via anonymous ftp. This package is designed to plot 2D representation of molecular orbitals from given molcular coordinates and orbital coefficients. It supports semi-empirical, STO-3G, 3-21(++)G(**) and 6-31(++)G** basis sets. It consists of three subprograms 'PSI1', 'PSICON' and 'PSI2'. 'PSI1' is responsible for generation of 3D grid of wave function psi (hence it was named 'PSI'). PSICON reads in the 3D grid and generates contour lines (isovalued lines in x,y,z directions). Finally 'PSI2' reads in these contour lines, performs hidden-line removal and gives plots for HPGL, PostScript, etc. 2. What are the typical methods of getting molecular orbital coefficients? Any semi-empirical and ab initio package should output orbital coefficients. I'm focusing only to the Gaussian ab initio package. In calculations with Gaussian, orbital coefficients can be obtained mainly in three ways. 1) %chk=filename If '%chk=filename' is specified in the zmatrix, a checkpoint file is created in the calculation. It'll contain all necessay information to generate input files for the PSI88. A utility called 'chk2psi' is provided in PSI88 distribution for this purpose. 2) POP=FULL If the keyword 'POP=FULL' is used in the zmatrix, MO cofficients are printed in the Gaussian output file. Usually the last occurrenct of "Molecular Orbital Coefficients' are the coefficients of the final optimized geometry. 3) FORMCHECK=ALL If the keyword 'FORMCHECK=ALL' is used in the zmatrix, a formcheck file is created in the calculation. It contains coordinates, orbital energies, orbital coefficients, etc. Since this file contains most reliable information on molecular orbitals, I recommend anyone to use formcheck files for creating PSI88 input files. An nawk script 'fchk2psi' (which I'm going to enclose here) can be used for this purpose. 3. What utilities are available for generating input files for the PSI88 package from Gaussian-related files? 1) chk2psi This is written to generate PSI88 input files from a Gaussian check- point file. However, cautions should be taken before its use, i.e., it always extracts the Z-matrix orientation and may give wrong MO plots. Note that this comes with the PSI88 distribution. 2) g2psi I wrote a utilty which extracts molecular coordinates and oribtal coefficients from a Gaussian output which has been executed with POP=FULL option. Interested users may want to contact me to get it mailed to you. 3) fchk2psi This script is written in AWK programming language which is an inter- preted language and available in most UNIX systems as /usr/bin/nawk. It extracts molecular coordinates and MO coefficients from a formcheck file and creates input files for the PSI88 package. It will be found at the end of this posting. Users of the PSI88 should realize that the 'Standard' orientation of molecule must be used for plotting MO's IF IT EXISTS. Otherwise, the 'Z-matrix orientation' can be used instead. A formcheck file contains always the right molecular orientation for MO's. So I recommend everyone to use formcheck files for creating PSI88 input files. The name of the script is recommended to be 'fchk2psi'. The Usage is simply "fchk2psi filename". If filename has a suffix ".log", e.g., "file.log", PSI input file names will be "file.psi1", "file.psi2" and "file.psicon". Otherwise, "psi1", etc will be simply appended to the filename. If input for fchk2psi comes from standard input (stdin), e.g., "zcat filename.Z | fchk2psi" or "fchk2psi < filename", files named "tmp.psi1", "tmp.psi2" and "tmp.psicon" will be created. ____________________________________________________________________________ Using your favorite editor, carve out the script between 'CUT HERE' pairs. Name it 'fchk2psi' and make it executable by doing 'chmod +x fchk2psi'. Finally place it in a directory which is included in your evironment variable 'PATH'. --------------------- CUT HERE -------------------------------------------- #!/usr/bin/nawk -f # @(#) fchk2psi: extracts molecular coordinates and MO coefficients # from Gaussian formchekpoint file and creates input files for # the PSI88 package written by Prof. William Jorgensen and Dr. # Dan Severance at Yale University. # To get MO coefficients from Gaussian, specify FORMCHECK=ALL. # # Usage: fchk2psi filename # Author: Dongchul Lim # Department of Chemistry, Yale University # lim@rani.chem.yale.edu BEGIN { natoms = 0; # number of atoms nbasis = 0; # number of basis functions bohr2A = 0.529177; # Bohr to Angstrom conversion factor number = "^[-+]?([0-9]+[.]?[0-9]*|[.][0-9]+)([eE][-+]?[0-9]+)?$"; getline; # 1st line (ignore) getline; # 2nd line (contains basis set) basis = substr($0,35,20); # basis set sub(/^[ \t]+/, "", basis); # remove preceding spaces and tabs if (FILENAME == "-") { # standard input file_psi1 = "tmp.psi1"; file_psi2 = "tmp.psi2"; file_psicon = "tmp.psicon"; } else { file = FILENAME; sub(/\.log$/, "", file); # replace ".log" by "" file_psi1 = sprintf("%s.psi1", file); file_psi2 = sprintf("%s.psi2", file); file_psicon = sprintf("%s.psicon", file); } if (Debug) { printf("basis = %s\n", basis); printf("psi1 = %s\n", file_psi1); printf("psi2 = %s\n", file_psi2); printf("psicon = %s\n", file_psicon); } } /Number of basis functions/ { nbasis = substr($0,50,20) + 0; } /Number of atoms/ { natoms = substr($0,50,20) + 0; } /Atomic numbers/ { n = 0; while (getline > 0 && match($1,number)) { for(i=1;i<=NF;i++) {n++; an[n] = $i+0;} } } /Current cartesian coordinates/ { n = 0; while (getline > 0 && match($1,number)) { for(i=1;i<=NF;i++) {n++; xyz[n] = $i * bohr2A;} } } /Alpha MO coefficients/ { print_psi1(xyz, an, natoms, basis, file_psi1); n = 0; while (getline > 0 && match($1,number)) { for(i=1;i<=NF;i++) { n++; mo[n] = $i+0; if (n == 8) { print_mo(mo,n, file_psi1); n = 0; } } } print_mo(mo,n, file_psi1); } END { if (natoms == 0) { printf("\007No atoms found.\n"); exit; } # psi1 has been already printed. So output just psi2 and psicon. print_psi2(xyz, an, natoms, basis, file_psi2); print_psicon(basis, file_psicon); } function print_mo(mo, n, file, i) { for(i=1;i<=n;i++) printf("% 10.6f", mo[i]) > file if (n>0) printf("\n") > file } function print_psi1 (xyz, an, natoms, basis, file) { printf("%s\n", basis) > file printf("AUTO0\n") > file printf("0101 1.0\n") > file printf("0\n") > file print_coord(xyz, an, natoms, file); printf("99\n") > file } function print_coord (xyz, an, natoms, file, i) { for(i=0;i file } } function print_psicon (basis, file) { printf("%s\n", basis) > file printf(" 1 1 0 1\n") > file printf(" 0.075000\n") > file } function print_psi2 (xyz, an, natoms, basis, file) { printf("%s\n", basis) > file printf("SUBTITLE\n") > file printf("010000 1.0\n") > file printf("00\n") > file print_coord(xyz, an, natoms, file); printf("99\n") > file printf(" 61.1000 132.1000 1.1000 0.8500\n") > file printf("02\n") > file } --------------------- CUT HERE -------------------------------------------- From hughc@extro.ucc.su.oz.au Tue Jul 26 23:56:44 1994 Received: from extra.ucc.su.OZ.AU for hughc@extro.ucc.su.oz.au by www.ccl.net (8.6.9/930601.1506) id XAA24785; Tue, 26 Jul 1994 23:50:10 -0400 Received: from hugh (hugh.pharmacol.su.OZ.AU [129.78.41.50]) by extra.ucc.su.OZ.AU (8.6.8.1/8.6.6) with SMTP id NAA06494 for ; Wed, 27 Jul 1994 13:50:31 +1000 Message-Id: <199407270350.NAA06494@extra.ucc.su.OZ.AU> X-Sender: hughc@postbox.su.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 27 Jul 1994 13:51:20 +1100 To: chemistry@ccl.net From: hughc@extro.ucc.su.OZ.AU (Hugh Capper) Subject: Gaussian & Cray YMP/EL X-Mailer: Dear CCLers, Can anybody help me as to the functionality and preformance of Gaussian on a Cray YMP/EL with 256 Mbytes RAM. I am looking for some rough idea of the turn around time for fairly simple jobs. Best Wishes, Hugh Capper