From NOINVILLE@CECM.glvt-cnrs.fr Fri Oct 21 10:22:22 1994 Received: from mailimailo.cicb.fr for NOINVILLE@CECM.glvt-cnrs.fr by www.ccl.net (8.6.9/930601.1506) id KAA24698; Fri, 21 Oct 1994 10:04:28 -0400 X400-Received: by /PRMD=cicb/ADMD=atlas/C=FR/; Relayed; 21 Oct 94 15:01:22+0100 X400-Received: by /PRMD=GLVT-CNRS/ADMD=ATLAS/C=FR/; Relayed; 21 Oct 94 14:05:06 GMT Date: 21 Oct 94 14:05:06 GMT From: NOINVILLE Message-ID: <8030041521101994/A00781/CECM01/118AABC32700*@MHS> To: chemistry@ccl.net Subject: Mopac Executable for IBM RS/6K Importance: Normal Sensitivity: Company Autoforwarded: False Hi Netters, A friend fo mine is looking for an executable MOPAC file because he doesn't have any FORTRAN compiler. It think that MOPAC is public domain so may be some of you could help locate such a file on the net. This is for an IBM RS/6000. Thanks in advance, Vincent *********************************************************** * Vincent NOINVILLE || * * Laboratoire de Physicochimie des Biopolymeres * * 2, Rue Henri Dunant - 94320 THIAIS - FRANCE * * Tel. (33 1) 49 78 11 20 * Fax. (33 1) 49 78 13 23 * * E-mail: noinville@glvt-cnrs.fr * *********************************************************** From markm@portal.vpharm.com Fri Oct 21 11:21:51 1994 Received: from portal.vpharm.com for markm@portal.vpharm.com by www.ccl.net (8.6.9/930601.1506) id KAA25521; Fri, 21 Oct 1994 10:58:47 -0400 Received: by portal.vpharm.com (AIX 3.2/UCB 5.64/4.03) id AA16945; Fri, 21 Oct 1994 10:56:15 -0400 From: markm@portal.vpharm.com (Mark Murcko) Message-Id: <9410211456.AA16945@portal.vpharm.com> Subject: calculating bond orders and atom types To: chemistry@ccl.net Date: Fri, 21 Oct 1994 10:56:14 -0500 (EDT) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 371 In the opinion of the group, what are currently the best methods available to assign bond orders and bond types? We've tried both Quanta and Insight with limited success. Certain bond types are often or always messed up. Are there other programs which people find to be more reliable? Thanks for any help, and I'll summarize responses. / Mark (markm@vpharm.com) From raman@bioc01.uthscsa.edu Fri Oct 21 11:28:59 1994 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.9/930601.1506) id KAA25122; Fri, 21 Oct 1994 10:33:29 -0400 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Fri, 21 Oct 1994 9:35:57 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA12451; Fri, 21 Oct 94 09:33:38 CDT From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9410211433.AA12451@bioc01.uthscsa.edu> Subject: Re: CCL:Ribbons & Renderman To: C1790@SLVAXA.UMSL.EDU (BILL WELSH) Date: Fri, 21 Oct 1994 09:33:35 -0500 (CDT) Cc: chemistry@ccl.net In-Reply-To: <01HII88OB7Y0AKTJG8@SLVAXA.UMSL.EDU> from "BILL WELSH" at Oct 20, 94 04:34:54 pm X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 851 Bill: > 1) Mike Carson's RIBBONS. You can reach Mike at: carson@gtx.cmc.uab.edu An academic license for Ribbons costs ~ $250. Cheers -raman -- C.S.Raman UNIX Programming & Administration SPARC & SGI Systems raman@bioc01.uthscsa.edu - INTERNET Department of Biochemistry raman@mintaka.chpc.utexas.edu - CHPC UTHSCSA c.raman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From ADAMSL@CSOVAX.PORTSMOUTH.AC.UK Fri Oct 21 13:21:54 1994 Received: from sun2.nsfnet-relay.ac.uk for ADAMSL@CSOVAX.PORTSMOUTH.AC.UK by www.ccl.net (8.6.9/930601.1506) id NAA28349; Fri, 21 Oct 1994 13:06:50 -0400 From: Message-Id: <199410211706.NAA28349@www.ccl.net> Via: uk.ac.portsmouth.csovax; Fri, 21 Oct 1994 17:13:30 +0100 Date: Fri, 21 Oct 94 17:13 GMT To: CHEMISTRY Subject: MacroModel Dear all, Could someone please send me some information concerning MacroModel, particularly the price to academics? Lesley Adams Centre for Molecular Design University of Portsmouth U.K. From cmartin@rainbow.uchicago.edu Fri Oct 21 13:31:52 1994 Received: from midway.uchicago.edu for cmartin@rainbow.uchicago.edu by www.ccl.net (8.6.9/930601.1506) id MAA27942; Fri, 21 Oct 1994 12:47:55 -0400 Received: from rainbow.uchicago.edu by midway.uchicago.edu for chemistry@ccl.net Fri, 21 Oct 94 11:47:27 CDT Received: by rainbow.uchicago.edu (931110.SGI/930416.SGI) for @midway.uchicago.edu:chemistry@ccl.net id AA07239; Fri, 21 Oct 94 13:04:45 -0500 From: cmartin@rainbow.uchicago.edu (Charles Martin) Message-Id: <9410211804.AA07239@rainbow.uchicago.edu> Subject: new gromos To: chemistry@ccl.net Date: Fri, 21 Oct 1994 13:04:45 -0600 (CDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 694 Hi A colleague of mine is using GROMOS for his research, but has many problems because it is written in Fortran-66, has no GUI. Does anyone know of a code which has similar features to GROMOS, has a GUI, and has available source code? Thanks Chuck ================================================================== Charles H. Martin email: chm6@quads.uchicago.edu US Mail: c/o Freed Group The James Franck Institute and The Department of Chemistry The University of Chicago 5640 South Ellis Avenue Chicago, Illinois 60637 Work: (312) 702-3457 Fax: (312) 702-5863 ================================================================== From gmeier@ncsa.uiuc.edu Fri Oct 21 13:39:58 1994 Received: from newton.ncsa.uiuc.edu for gmeier@ncsa.uiuc.edu by www.ccl.net (8.6.9/930601.1506) id MAA28114; Fri, 21 Oct 1994 12:56:39 -0400 Received: from [128.254.136.231] by newton.ncsa.uiuc.edu with SMTP id AA05741 (5.65a/IDA-1.4.2 for CHEMISTRY@ccl.net); Fri, 21 Oct 94 11:56:33 -0500 Message-Id: <9410211656.AA05741@newton.ncsa.uiuc.edu> X-Sender: u34065@141.142.2.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 21 Oct 1994 13:00:26 -0600 To: CHEMISTRY@ccl.net From: gmeier@ncsa.uiuc.edu (Gary Meier) Subject: Conversion of Wiswesser Line Notations-SUMMARY I recently posed the question: "I would like to find a program or utility that can translate Wiswesser Line Notations into some other format. Does anyone know of a way to automatically generate, for example, a connection table from an WLN?" A summary of the replies follows. Thanks to all who responded. *********************************************************************** MDL markets (or used to market...) a program WLNCT, which was derived from a program developed at Pomona College, in Al Leo's group. Your company has used MDL software in the past - you might check if you have an old copy of WLNCT around. If not, you could either contact MDL (phone 800-326-3002, email techsupp@mdli.com) or check with Al Leo (909-621-8452) to see if he has an old copy around. The original code from Leo was in PL. Dough@mdli.com ************************************************************************* MDL used to sell a program called WLNCT which would convert WLNs to MDL MOL file format. Jim +------------------------------------------------------------------------+ | Jim Bentley, Ph.D. || Internet: jbentley@bwco.com | ************************************************************************** I posted a similar query some time ago and found only an obsolete program by Molecular Design Inc which they still wanted $10K for!!! Please send me any useful info you obtain. Cheers, Dave D.Winkler@chem.csiro.au __________________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 ***************************************************************************** Some years ago we used CROSSBOW (developed, I think, by Fraser Williams) to convert a large WLN file into connection table format. It worked ! You will probably receive more current information from other CCL users, but if not let me know and I will follow this up. Sue Jackson (susan.jackson@roche.com) Head of Information Centre Roche Products Ltd ******************************************************************************* I don't know if they can, but a good try would be Daylight Chemical Information Systems support@daylight.com. Otherwise, contact Peter Willett: "P.Willett@sheffield.ac.uk" Yvonne Martin Abbott Laboratories ******************************************************************************* Gary, The best program is probably the Dearing(sp?) program that used to be available from Frazer-Williams in England. Dr. Trevor Devon at Pfizer in Sandwich England wrote a similar program that we used back in 1982 to convert our corporate database from WLN to MACCS but I don't know how general it is or what its availability is. Beryl Dominy bwdominy@pfizer.com ******************************************************************************* Hello Gary, Jure Zupan of the National Institute of Chemistry in Ljubljana, Slovenia has written programs that translate WLN. His email account should be jure.zupan@ki.si An alternative account of one of his colleagues is marko.razinger@ki.si Jure may be away from his lab but I know that Marko is present. (and he reads his email) Mark Madison madison@asu.edu ****************************************************************************** As you may have been told already --- Daylight Chemical Information Systems and/or BioByte Corp. should be able to provide software to convert from WLN to SMILES and various other CT representations. ....... BioByte Corp. is actually a "spin-off" from Daylight. The letterhead says that Al Leo is the President and Corwin Hansch is the CEO (or something like that). As you probably know, Al Leo is "the CLOGP guy" and was the reason for which Dave Weininger developed what is now the Daylight software. BioByte was formed so that the CLOGP-related functionality can be sold separately from Daylight's datbase-related functionality. I have done a little check for you and it appears to me that the standard BioByte distribution tape does not include WLN input conversion. HOWEVER, I am 100% certain that Al Leo has software to do that conversion. Indeed, his database of experimental logP values was originally organized by WLN and conversion to SMILES was one of the first tasks to be performed. I suggest that you telephone him. His number is 909-621-8452. Hope this helps. Regards, Bob PEARLMAN@VAX.PHR.UTEXAS.EDU ****************************************************************************** > Cobra from Oxford Molecular Terrapin House South Parks Road Oxford OX1 3UB England will do this. Cheers Jeffrey J Gosper ******************************************************************************** Gary Meier, Ph.D. Senior Research Computational Scientist FMC Corporation, Agricultural Chemical Group Box 8 Princeton, NJ 08543 (609) 951-3448 (gmeier@ncsa.uiuc.edu) From markm@portal.vpharm.com Fri Oct 21 14:21:55 1994 Received: from portal.vpharm.com for markm@portal.vpharm.com by www.ccl.net (8.6.9/930601.1506) id NAA28995; Fri, 21 Oct 1994 13:53:22 -0400 Received: by portal.vpharm.com (AIX 3.2/UCB 5.64/4.03) id AA17207; Fri, 21 Oct 1994 13:50:49 -0400 From: markm@portal.vpharm.com (Mark Murcko) Message-Id: <9410211750.AA17207@portal.vpharm.com> Subject: CCL:calculating bond orders and atom types (fwd) To: chemistry@ccl.net Date: Fri, 21 Oct 1994 13:50:48 -0500 (EDT) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 1046 I'd like to clarify what I was asking for earlier today. I said: > In the opinion of the group, what are currently the best methods > available to assign bond orders and bond types? We've tried > both Quanta and Insight with limited success. Certain bond types > are often or always messed up. Are there other programs which > people find to be more reliable? I now realize from several of the responses I've received that my question was ambiguous. I am _not_ looking for a QM solution -- unless it is _very_ fast. I will need to perform this bond-order checking on hundreds of molecules, maybe thousands. Several of the responses I've received concern Bader analysis, Meyer analysis, etc. These are very interesting approaches (some of which I knew about, and some I didn't) but I don't think they will help me in the current situation. More likely, the solution will be some kind of rule-based approach that analyzes the bonding and geometries of the molecules. Sorry for the confusion and I'm still seeking the perfect answer! From shenkin@still3.chem.columbia.edu Fri Oct 21 15:21:57 1994 Received: from still3.chem.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.9/930601.1506) id OAA29692; Fri, 21 Oct 1994 14:35:15 -0400 Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for CHEMISTRY@ccl.net id AA07429; Fri, 21 Oct 94 14:34:40 -0400 From: "Peter Shenkin" Message-Id: <9410211434.ZM7427@still3.chem.columbia.edu> Date: Fri, 21 Oct 1994 14:34:29 -0400 In-Reply-To: "CCL:MacroModel" (Oct 21, 5:13pm) References: <199410211706.NAA28349@www.ccl.net> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: , CHEMISTRY Subject: Re: CCL:MacroModel Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Oct 21, 5:13pm, wrote: > Subject: CCL:MacroModel > Could someone please send me some information concerning MacroModel, > particularly the price to academics? Hope the following is helpful; please contact Joan Horgan directly for pricing info. -P. ========================================================================== INTRODUCTION TO MACROMODEL 4.5 September 21, 1994 [[ You may obtain the latest version of this document remotely by means of "finger mmod@still3.chem.columbia.edu". ]] Note: MacroModel 5.0, due for release in early 1995, is in progress. The SGI version will almost certainly require IRIX 5.x. If this is a problem, let us know. We are now shipping Version 4.5 of MacroModel / BatchMin. This version is supported on SGI and on IBM RISC hardware; BatchMin is supported on several additional platforms. This document contains the following sections: GETTING FURTHER INFORMATION: Whom to contact for ordering information or for answers to technical questions. NEW FEATURES IN VERSION 4.5: Brief list of changes between version 4.0 and 4.5. This section will be of greatest interest to users familiar with previous versions. PRODUCT DESCRIPTION (as of Version 4.0): Brief description of the capabilities of the MacroModel, BatchMin and XCluster programs. (These three programs are supplied as part of MacroModel) NEW FEATURES IN VERSION 4.0: Differences between version 3.5 and 4.0. GETTING FURTHER INFORMATION: For ordering or pricing information for academic, government and non-profit sites, please contact: Ms. Joan Q. Horgan FAX: (212) 854-5429 or 678-9039 Voice: (212) 854-8665 Email: jqh@still3.chem.columbia.edu Address: Box 663 Havemeyer Hall Department of Chemistry Columbia University New York, NY 10027 Prospective industrial users should contact: Dr. Dan Chodosh / Distributed Chemical Graphics Voice: (215) 885-3706 FAX: (215) 355-0954 Please address technical questions to: mmod@still3.chem.columbia.edu (note new host name!) FAX: (212) 678-9039 Voice: (212) 854-8402 (MacroModel) Voice: (212) 854-5143 (BatchMin) You may also address questions or share your experiences with the MacroModel user community by means of the MacroModel computer mailing list: mmodinfo@uoft02.utoledo.edu (Note: "02" is "zero two".) Before doing so, you should subscribe to the list by sending mail that includes the line, "subscribe mmodinfo", to the address: mmodinfo-request@uoft02.utoledo.edu NEW FEATURES IN VERSION 4.5 (in addition to various bug-fixes): Front-end (MacroModel) features: * MIPCAPI (MacroModel Inter-Process Communication Application Interface) provides a library by means of which programs written by users may utilize MacroModel as a graphical front end * 1-D plots of energy vs. torsion angle * Ribbon diagrams for proteins * Visualization panels for associating specific energetic interaction terms in the molecule with specific lines in the force-field * Panel for more easily performing operations on sets * Panel for doing volume calculations on molecules * Panel for setting up BatchMin MC/SD calculations (see below) * Button for setting up Monte-Carlo-Single-Minimum conformational searches * Greater control and configurability of color scheme * Movies from dynamics sampling now retain colors * Ability to manually alter PDB chain, residue and atom names Back-end (BatchMin) features: * Free-energy perturbation; works with mixed-mode Monte-Carlo / Stochastic Dynamics, as well as with SD or MD. Implemented for network-distributed execution, if desired. * Facilities for re-initializing conformational searches from the output of previous, incomplete searches, and for obtaining interim summaries of the progress of a search, so far. * "ASET" command for defining sets of atoms, and printing energetic contributions within and between the sets. * User-definable atom types, read in at run-time. We supply new types and force-field components for alkali metal cations, but users can also add their own types, and supply parameters for these types in the force- field. * Additional capabilities for handling geometry-dependent force-field parameters. This will be useful mostly for transition-state modeling. MM2* additions: Force-field parameters for transition-state models of activated Diels-Alder reactions, nitrileoxide additions (K. Houk); sulfonamide parameters (G. Poli); more parameters for boron-containing transition states (A. Bernardi). AMBER* and OPLSA* addition: pyranose parameter revision for acetal anomeric equilibrium (Q. McDonald); new parameters based on unpublished work by P. Kollman (UCSF) for gem diethers such as dimethoxymethane. PRODUCT INFORMATION: MacroModel is the generic name for a set of molecular modeling tools; it actually consists of several separate programs. MacroModel itself is a visualization tool for building, examining and manipulating organic and biological molecules. It can read and write molecular files in its own format, as well as in the format specified by the the Protein Data Bank at Brookhaven National Laboratories. A number of other programs are capable of writing MacroModel format files; these include Gaussian-92 and Chem-3D. BatchMin is a separate program which carries out molecular mechanics. Most users are never aware of the separate existence of BatchMin, since most BatchMin jobs are set up, and the results monitored, by means of its interface with MacroModel. Thus, most users think of MacroModel and BatchMin as one; we will refer to them together as "MacroModel" in the rest of this description. One of MacroModel's strengths is the fact that it provides the user with a choice of implementations of the AMBER, MM2, MM3, and OPLS force-fields. The force-field which has been best parameterized for the system in question can be used (MM3 for gas-phase study of hydrocarbons, AMBER for peptides and nucleic acids, OPLS for solvated organic molecules). The force-field of choice is read in at run- time; its file format is such that the user can alter general parameters at will, or add parameters for molecular substructures which have either no parameters or only poorly defined parameters. For example, charge distributions derived by the user from ab-initio quantum studies on a system of interest can be used in MacroModel to perform molecular-mechanics studies of the same system, instead of using the force-field's default parameters. A list of molecular mechanics procedures supported by MacroModel follows. For each method, the user may select from among the choices given in parentheses. In most cases the program selects a reasonable default if an explicit choice is not made. Conformational search (systematic; Monte-Carlo) Energy minimization (steepest descent; variable metric; conjugate gradient; truncated Newton; full-matrix Newton-Raphson) In multiple structure minimization mode, the program eliminates duplicate output structures from the results of minimizing a sequence of input structures. Monte Carlo sampling Molecular dynamics (constant energy; constant temperature; bath-coupled stochastic dynamics) SHAKE is available. Mixed-mode Monte Carlo / Stochastic Dynamics. This is a procedure developed here which speeds up the sampling of conformational space during a dynamics run generating a canonical ensemble. Solvation. We provide a continuum model of solvation known as the Generalized Born / Surface Area (GB/SA) model. This provides good approximations to relative solvated energies at a computational cost much lower than that of explicit solvent models. We provide parameterization for water and for chloroform. Free-energy perturbation, in the context of implicit solvent and mixed-mode SD/MC. XCluster performs cluster analysis on molecular conformations. For example, the structures resulting from a conformational search may be examined to determine whether they fall into distinct classes. Though a separate process, this program is equipped to communicate with a running MacroModel process. For example, a subset of atoms to be compared for conformational similarity may be "picked" from the MacroModel interface and automatically passed to XCluster. In all of these, as well as new procedures being developed, we are committed to full disclosure of methods and parameters by means of prompt publication. MacroModel runs on Silicon Graphics or IBM/RS 6000 hardware equipped with GL graphics. Minimum suggested hardware requirements are: SGI: 32 Mb main memory, 1.2 Gb disk drive. IBM: 64 Mb main memory, 1.2 Gb disk drive. If you plan to study large molecules, such as proteins, we recommend that you configure your system with 100 Mb of swap space. ----------------------------------------------------------------------- For MacroModel to run on an SGI machine you need to have (in addition to the standard libraries) the following software products loaded: C++ run-time environment (to use the Force Field Parameter Viewer) ----------------------------------------------------------------------- For IBM machines we support the following graphics adapters: 24 bit Sabine with zbuffer or 24 bit gt4x with zbuffer. We do not guarantee that other boards will work properly. For MacroModel to run on an IBM RS/6000 you need to have the following software products loaded: X/Motif run-time environment FORTRAN run-time environment GL run-time environment C++ run-time environment (to use the Force Field Parameter Viewer) These products may be purchased from IBM. NEW FEATURES IN VERSION 4.0: MacroModel Version 4.0 includes the following new features: Front-end (MacroModel) features: * Improved Help facility * Ramachandran plots * Ability to analyze ensembles of structures based on miscellaneous collective features (e.g., centroid of a group of atoms) * "Filter panels" providing the ability to select structures meeting user-defined selection criteria from a file of multiple conformations. * Support for hardware stereo on SGI * Improved conversion to and from PDB format files Back-end (BatchMin) features: * Support for monitoring H-bonds during dynamics * Mixed mode Molecular Dynamics / Monte Carlo * Network-distributed parallel processing for conformational search and multiple minimization * Built-in tools for static memory analysis * Improved tools for source-code maintenance (relevant only to industrial source-code customers) XCluster: * An entirely new program, XCluster, which performs cluster analysis on ensembles of molecular conformations -- *********** World music: What bluegrass is to a Bulgarian. ********** *Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ.,* * New York, NY 10027; shenkin@columbia.edu; (212) 854-5143 * ************ Alphabetical order makes strange bedfellows. ************ From palres.dnet.sandoz.com!bowlus@sandoz.com Fri Oct 21 17:24:21 1994 Received: from tigger.jvnc.net for palres.dnet.sandoz.com!bowlus@sandoz.com by www.ccl.net (8.6.9/930601.1506) id QAA02394; Fri, 21 Oct 1994 16:57:11 -0400 Received: from sndzeh.UUCP by tigger.jvnc.net with UUCP id AA14087 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Fri, 21 Oct 1994 16:57:10 -0400 Message-Id: <199410212057.AA14087@tigger.jvnc.net> Date: Fri, 21 Oct 94 16:47:07 -0400 From: bowlus@palres.dnet.sandoz.com (Steve Bowlus) To: "chemistry@ccl.net"@SNDZEH.dnet.sandoz.com Cc: BOWLUS@sandoz.com Subject: AMSOL performance I am running Amsol 4.5 on an Indigo2 (150Mhz), trying to do solvation energies of compounds with ca. 15 heavy atoms. These systems optimize for the gas phase in about 2 cpu minutes using the keyword "AM1". For the solvation, I am using "AM1 SM2" and 4 cpu _hours_ later, things are still chugging along. I have no experience with the solvation models, and would like know what order of magnitude of cpu times I should be expecting. Also , are there keyword combinations which will reduce this (I haven't tinkered with e.g. PULAY, since the gas phase calculation went so quickly)? If there is interest for information on Amsol performance, I will summarize to the net. sb =========================================================================== Stephen B. Bowlus, Ph.D. Computer-Aided Molecular Design Research Division e-mail: bowlus@sandoz.com Sandoz Agro, Inc. Phone: + 1 415 354 3904 975 California Ave. Fax: + 1 415 857 1125 Palo Alto, CA 94304 =========================================================================== From rerocha@fox.cce.usp.br Fri Oct 21 18:25:29 1994 Received: from bee.uspnet.usp.br for rerocha@fox.cce.usp.br by www.ccl.net (8.6.9/930601.1506) id RAA02776; Fri, 21 Oct 1994 17:32:41 -0400 Received: from fox.cce.usp.br (fox.cce.usp.br [143.107.70.1]) by bee.uspnet.usp.br (8.6.8.1/SPARC10-CCE2.0)id UAA20768 Received: from localhost (rerocha@localhost) by fox.cce.usp.br (8.6.4/CONVEX120-CCE2.0) id TAA08200 Date: Fri, 21 Oct 1994 19:32:10 -0200 From: Reginaldo Cesar Rocha Message-Id: <199410212132.TAA08200@fox.cce.usp.br> To: chemistry@ccl.net Subject: About Mathematica I'm a chemistry student and I want to use the Mathematica for didactic purposes in Quantum Chemistry, particularly in 3D simulation, for example in orbitals construction. I have the Mathematica version 2.0 on PC 486. I know that there are some packages available. I'd like to know how to get them. I'd be very grateful too if you could suggest some readings about this subject. Thanks in advance, Reginaldo. From jgilbert@du.edu Fri Oct 21 19:21:59 1994 Received: from mercury.cair.du.edu for jgilbert@du.edu by www.ccl.net (8.6.9/930601.1506) id SAA03549; Fri, 21 Oct 1994 18:59:58 -0400 Received: (from jgilbert@localhost) by mercury.cair.du.edu (8.6.9/8.6.9) id RAA24401; Fri, 21 Oct 1994 17:01:30 -0600 Date: Fri, 21 Oct 1994 17:01:27 -0600 (MDT) From: JULANNA V GILBERT Subject: spartan/gaussian To: chemistry@ccl.net cc: JULANNA V GILBERT Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Oct.10/1994 I requested help in printing the pictures generated by Spartan running on a RS/6000 Power PC onto a postscript printer. I received numerous responses. Several people suggested using screen grabber programs that are accessible from the internet. So far, we have tried: xv, xgrab and collage xv and xgrab can be found at ftp.x.org (a standard depository for x software). collage was found at an NCSA center (we used Mosaic to find it). Of these three, collage is the least cumbersome to use and gives fine output. We are still experimenting with the colors that give the best results on our non-color HP laser printer. Of course, since these are all screen grabbers, you are limited by the resolution of the screen, and although the pictures are not truely fantastic, we feel that they are pretty good, and could probably be used in a journal publication since the picture would be greatly reduced in size for printing in the journal anyway. Wavefunction (the company that wrote and sells Spartan) and other people told me that version 4 of Spartan will have printing capabilities so that users won't have to use these screen grabbing techniques. (An upgrade does cost some bucks, so we may not be able to take advantage of the new version until our ship comes in.) Other suggestions that were made but that we have not tried are: xwd with xpr, x24wd, kapture (from IBM UK, cost = 400 pounds) gemm and rasmo, imagemagick. I still have the specific email messages sent to me on these other screen grabbers, and will forward them to anyone who is interested. Thank you to everyone for your information!!! Julanna Gilbert University of Denver From vazquez@iqm.unicamp.br Fri Oct 21 20:21:58 1994 Received: from kalypso.iqm.unicamp.br for vazquez@iqm.unicamp.br by www.ccl.net (8.6.9/930601.1506) id TAA04032; Fri, 21 Oct 1994 19:48:58 -0400 Received: (vazquez@localhost) by kalypso.iqm.unicamp.br (8.6.8/8.3) id UAA01553; Fri, 21 Oct 1994 20:21:29 -0300 From: Pedro A M Vazquez Message-Id: <199410212321.UAA01553@kalypso.iqm.unicamp.br> Subject: Re: CCL:About Mathematica To: chemistry@ccl.net, marcia@sloop.cpac.washington.edu, rerocha@fox.cce.usp.br Date: Fri, 21 Oct 1994 20:21:28 -0300 (GMT-0300) Organization: Instituto de Quimica Unicamp X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 822 Reginaldo Cesar Rocha said: > > > > > I'm a chemistry student and I want to use the Mathematica for didactic > purposes in Quantum Chemistry, particularly in 3D simulation, for example in orbitals > construction. I have the Mathematica version 2.0 on PC 486. I know that there are > some packages available. I'd like to know how to get them. I'd be very grateful too > if you could suggest some readings about this subject. > > > Thanks in advance, > > Reginaldo. > Hello Please contact Dr. Marcia Ferreira at marcia@sloop.cpac.washington.edu, she developed an undergraduate course on Quantum Chemistry using Mathematica and published the results in Quimica Nova last year. You can see some of the produced pictures pointing your WWW browser to http://www.iqm.unicamp.br/art/art-chem.html Regards Pedro