From rupley!local@cs.arizona.edu Thu Nov 19 07:35:05 1992 Date: Thu, 19 Nov 92 07:35:05 GMT From: rupley!local@cs.arizona.edu Message-Id: <9211190735.AA29070@rupley> To: CHEMISTRY@ccl.net Subject: coordinates for ideal helix, sheet, etc Are there available, preferably for anon ftp, coordinate sets for idealized protein secondary structure elements. I know I can build them, but I need them quickly. Thanks, John Rupley Biochemistry rupley@cs.arizona.edu From UDIM018@FRORS31.bitnet Mon Nov 19 08:33:38 1992 Message-Id: <199211191214.AA19136@oscsunb.ccl.net> Date: 19 Nov 92 12:33:38 EDT From: Subject: semiempirical calculations on Rydbergs To: chemistry@ccl.net E. M. EVLETH Dynamique des Interactions Moleculaires Universite Pierre et Marie Curie 4 Place Jussieu, Tour 22, Paris 75005 33-1-44-27-42-08 (work), 33 = France; 1 = Paris 33-1-45-48-67-20 (home) FAX 33-1-44-27-42-17 e-mail UDIM018 at FRORS31 Charles Martin request for information on when semiempirical calculations work and don't. I'll share this following comments with the general community. In the area of calculating Rydberg states, efforts were abandonned years ago. Salaub and Sandorfy published a RCNDO-CI method in Theoretica Chemica Acta 20, 227 (1971) and Haque in JCP 67 3629 (1977). It should be first stated that there are NO valence excited states for simple molecules like methane and ammonia, the lower saturated hydrocarbons and possibly ANY molecule whose first excited state lies within a couple of eV of the first ionization state (see Robin's volumes on the Higher Excited States of Polyatomic Molecules). Even the pi-pi* state of ethylene is half 3-d Rydberg by computation if one uses a (correct) basis set having Rydberg components. The two papers cited above assigned almost complete valence character to the first excited states of methane and ammonia, which is wrong, experimentally or using ab initio calculations even at the STO-3G enriched with a single 3S rydberg orbital. Having seen this we approched the problem in 1980 (3rd cycle thesis of Z. D Hamoutahra, U of Bordeaux) and attemped to parameterized the CNDO-CI method with respect to ab initio calculations using a scheme close to that explained by Salaub and Sandorfy. We found that minor variations in parameterizing a Rydberg resonance coupling parameter yield states having about the same excited energy but swinging wildly from being valence to Rydberg in character. We came to the the conclusion that the parameterization was intrinsically unstable and that a universal set of parameters useable for explaining, for instance, the Rydberg character of the first excited states of all the alkylamines up to DABCO and ABCO (unusual tricyclic amines that Halpern has characterized their fluorscence lifetimes and yields) was impossible. Angelo Rossi was able to do this using just a simple STO-3G+3S basis. Conclusion--don't waste your time--semiempirical theory is definitely a looser in this area. I did not published any of this thesis work because I did not know about the Journal of Negative Results. Anybody like myself brought through the PPP-pi-electronic spectra, extended Huckel, CNDO-on pre-moderate size ab initio period would have an optimistic view of being able to succeed using SOME semiempirical approach to ANY problem. This is an article of faith. I lost my faith at that point. From IPMP500@INDYVAX.IUPUI.EDU Mon Nov 19 07:01:36 1992 Date: 19 Nov 1992 12:01:36 -0500 From: "Michael A. Peterson" Subject: Summary of responses to Word Proc. & Graphing on SGIs. To: chemistry@ccl.net Message-Id: <01GRC2LYKB9U004YOD@INDYVAX.IUPUI.EDU> Netters: I finally managed to put all of the responses together concerning Graphing and Word Processing on SGIs. It is rather long (~330 lines), even though responses asking for this info have not been included. A hearty thanks to all who responded! The original Posting: >Dear netters: > >I am looking for graphing and word processing programs for our SGIs. >Does anyone have favorites? We have a variety of SGIs ranging from a 4D70 >to INDIGOs. Such programs would save us a lot of hastle I believe. > >Since this will only effect owners of SGI machines (presumably), respond >directly to me (ipmp500@indyvax.iupui.edu), and, if the responses warrant >it, I will summarize for the net. > >Thanks in advance! > >Michael A. Peterson >Dept. of Chemistry >Indiana Univ.-Purdue Univ. @ Indianapolis (IUPUI) >Internet: ipmp500@indyvax.iupui.edu BITNET: ipmp500@indyvax > The Responses Begin: =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From: IN%"rupley!local@cs.arizona.edu" 5-NOV-1992 08:27:50.71 I use S, an AT&T product (via USL or affiliated AT&T division), also sold in enhanced form as SPlus, by StatSci, Seattle. The package is a high level language/environment for statistics, math and graphics. There are graphics drivers for postscript, X11, iris, fig, etc. For a description, see the book, The New S Language, by Becker, Chambers and Wilks, Wadsworth, 1988. The graphics in the text were of course produced under S. The AT&T sources compile cleanly on an SGI (Crimson and 4D30). The package is powerful, allowing easy massaging of data before plotting. Vector/matrix-based math (MATLAB stuff is in the package). John Rupley Biochemistry rupley@cs.arizona.edu =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From: IN%"balbes@osiris.rti.org" 5-NOV-1992 08:29:33.09 I beleive WordPerfect has a version that runs on SGI's, I seem to remember them announcing it a while back. Microsoft Word is my personal favorite, I use it on a Mac, but they may have an SGI version by now. You can call them at 800-426-9400. Good Luck! Lisa % This came directly from a computer and is not to be doubted or disbeleived. % Lisa Balbes Osiris Consultants balbes@osiris.rti.org 2229B Hedgerow Rd, Columbus, OH 43220 614-442-9850 FAX: 614-451-5860 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From: IN%"rickr@scripps.edu" 5-NOV-1992 08:35:59.01 Michael, Greetings. I use SGI provided SHOWCASE and for the most part have found it satisfactory for my needs for writing papers, reports, etc. It might be worth a try especially if I understand it correctly, it comes with the SGI operating system. Regards, Rick Ross rickr@ppg.scripps.edu PPG INdustries =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From: IN%"gabriel@jg1.bchem.temple.edu" 5-NOV-1992 08:45:38.24 Dear Michael, Mihalisin Associates, Inc. has a suite of programs called TempleGraph and TempleGo which runs on SGI machines. They can be reached at: 215-646-3814 (600 Honey Run Road, Ambler Pa., 19002). I would appreciate receiving a summary of the responses that you get. Sincerely, Jerome L. Gabriel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + + + Department of Biochemistry ******************* + + Temple University Medical School * * + + Molecular Modeling Facility * HAVE PROTEIN * + + * * + + Jerome L. Gabriel * ------- * + + 1-215-221-1517 * * + + 1-215-221-7536(FAX) * WILL MODEL * + + * * + + E-mail ******************* + + gabriel@jg1.bchem.temple.edu + + + + + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From: IN%"berkley@wubs.wustl.edu" 5-NOV-1992 08:53:56.42 Try "frame" or "frame-maker", a publication quality text processor that runs on most unix boxes. Very slick, but (yet another editor :-) berkley =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From: IN%"davis@nod.bms.com" 5-NOV-1992 10:25:07.40 Hi, I'm not sure this is what you are looking for, but I work quite happily doing my word processing with LaTeX, xdvi, and dvips and my graphics with xfig. In addition, the auc-tex package for the emacs editor makes composing the text easy, previews the document with a couple keystrokes using xdvi, and prints the document with a coule more keystrokes using dvips. PostScript figures generated by xfig can also be included in the LaTeX document using dvips. Malcolm =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From: IN%"richard@iris26.biosym.com" 5-NOV-1992 11:40:43.22 I have some suggestions on word processing. If you want a real word processor, FrameMaker seems to be the way to go. We use it here for all our documentation. It has fonts and other DTP features. If you want just a fancy editor (that saves ASCII text) I strongly recommend zip. It can be had for free by ftp from sgi.com (graphics/zip/). It looks and feels like jot (the editor bundled with SGI machines), but has many of the features of emacs without emacs hassles. I haven't found a good graphing package. I tried gnuplot, but needed gcc to compile and eventually just gave up. I am interested to see what you turn up in this area. *********************************************************** Richard D. Macdonald, Ph.D. voice: (619) 546-5527 Biosym Technologies internet: richard@biosym.com 9685 Scranton Road San Diego, CA 92121-2777 *********************************************************** =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From: IN%"lim@rani.chem.yale.edu" "Dongchul Lim" 5-NOV-1992 11:58:13.55 Hi, try IRIS ShowCase, which is a fairly powerful word processor and image editor. -DCL lim@rani.chem.yale.edu =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From: IN%"STOUCH@dino.bms.com" "TERRY R. STOUCH (609)252-5442" 5-NOV-1992 14:22:32.68 yes, please summarize. we do not routinely use any wordprocessing packages, but rather text processors like TeX and Troff. I've heard that Framemaker is a good wordprocessor, however. Also, once (if) the macintosh emulator is available, mac software should be runnable on the iris. regarding graphics: we heavily use the program Splus, which is a pretty powerful statistics/data analysis/graphing/spreadsheet type program. it is probably overkill (and overly expensive) if graphing is all you want to do, however. (Statistical Sciences, Inc 202-283-8802, mktg@statsci.com) Terry R. Stouch, Ph.D. Room H3812, Bristol-Myers Squibb Pharmaceutical Research Institute P.O. Box 4000, Princeton, NJ 08543-4000 Phone: (609)252-5442 FAX: (609)252-6030 email: Stouch@bms.com Telex: 4754082 BRMYSQ PRIN =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From: IN%"sauer@organik.uni-erlangen.de" "Wolfgang Sauer" 5-NOV-1992 16:20:07.10 Michael: Since before we got our Indigo(e?)s, virtually everthing was done on PCs, we decided to go for WordPerfect, which promises a smooth transfer of both files and 'look-and-feel' between ones PC at home and the SGI at work. But because this is a university and everything has to go through admin, we are still waiting for delivery ... You should probably also post this to the appropriate newsgroup (comp.sys.sgi, I think), for there should be more people doing this kind of thing rather than 'science'. Oops, just noticed the "graphing" part of the question: there are so many really good programmes available for free (i.e. by anonFTP), I know hardly anybody who really needs a commercial package (esp. since for the free ones you get the source ...). Over here we use hcvis (NCSA), gnuplot and Irisplot and you might also want to have a look at the sgi version of xvgr (that's what it's called on a SUN; I believe the name changed slightly ...). That should be it for the moment. All the best, Wolfgang Sauer. -- +======================================+=====================================+ | Wolfgang Sauer | | | Institut fuer Organische Chemie I | "You have to be three standard | | Henkestr. 42, D-8520 Erlangen, FRG | deviations away from a normal | | | personality to like UNIX." | | sauer@organik.uni-erlangen.de | | | Tel.: 49/0 - 9131 - 85 - 2952 | Morris Jones (C&T) | | Fax: - 9132 | | +======================================+=====================================+ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From: IN%"jas@medinah.atc.ucarb.com" 6-NOV-1992 09:24:40.34 Sorry I can't help you much with your question, other than to say we've looked at FrameMaker on a variety of platforms and were quite pleased with it, but we now have a corporate policy that mandates using MS Word on our Macs and PC's and discourages any WP on Unix workstations (I have both an RS/6000 550 and an SGI 4D/310 for doing computational chemistry, and a Mac for everything else). You might look at the Corel* products, though. . . (Deleted Stuff) . JACK A. SMITH ...................................................................... Union Carbide Corp. || Phone: (304) 747-5797 Advanced Technical Computing || FAX: (304) 747-5448 P.O. Box 8361 || S. Charleston, WV 25303 || Internet: jas@medinah.atc.ucarb.com =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From: IN%"conniem@zest.esd.sgi.com" 6-NOV-1992 18:57:17.09 Michael: I received your inquery from one of my colleagues. I handle Technical Publishing here at SGI. I am also a pretty heavy user of an Indigo for office applications. Your question is quite broad, so I am going to have to respond similarly. There are a number of word processing alternatives on the SGI and also many graphing alternatives - what you will use them for will determine whether you will like them. I also don't know how technical you want to get. Simple business graphics can be handled from the spread sheet WingZ from Informix. If you need 3D graphics with complex algorithms, Mathematica from Wolfram Research will do the job. Our finance people use both. There are also several statistic packages, like SAS that run on SGI. Most assume you are running IRIX 4.0 or above. For Word Processing, there are again choices. While Island Write, WordPerfect and others run on our platform, I personally use FrameMaker. I like it because it has the right balance of ease of use and power for when I need to do things like a Table of Contents or interesting formatting. It has also been especially designed on SGI to handle 24bit color. The only caveat: All of the publishing packages, including FrameMaker rely on X Windows. The 4D/70 XWindows performace might be too slow for you. More memory helps, but it still doesn't come close to the Indigo performance. If you have any more questions about FrameMaker, please email me. Connie Miller =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From: IN%"states@wucs1.wustl.edu" 7-NOV-1992 19:44:46.99 I use FrameMaker on Macs, Suns, SGIs, and PCs and have been very pleased with it. Positive features: - True binary file exchange between all platforms. - Good control over all aspects of page and text layout and formatting. - Good integration of text editing, page layout, and graphics. - Defined import language. With a little nawk or perl script you can import plots of data and graphics directly into your document and add annotation, change fonts, line widths etc. - Pretty good spelling checker. - Under OpenLook, imported PostScript figures are displayed in native mode (not sure about the SGI version). Gripes: - No thesaurus. - Limited support for bibliographic citations. Does not work with EndNote. - No way to export a document generically (such as RTF format) and ASCII export gets confused if the Frame document is at all complex. Makes it difficult to send documents to colleagues who are not using Frame. - Needs a large screen to work effectively. - Drawing tools OK, but could be better. Especially when compared to ShowCase or some of the Mac applications. Then again, you can always use the tool of your choice and import the figure. David States Institute for Biomedical Computing / Washington University in St. Louis =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From: IN%"aditya!raman@uunet.UU.NET" 10-NOV-1992 12:34:17.38 For word processing (TEXT processing) one of the best is Framemaker distributed by Frame TEchnologies. You can create top class documents, with graphic import and also with color features. If you want less sophisticated stuff, try TeX, troff and so on. These are a little more cumbersome to learn, but once you learn it, they are very useful. For graphics, depends on what you want to do. For simple slide preparation, you can use many tools under SHOWCASE, a software which usually comes with the SGIs. Good luck. .raman raman%aditya@uunet.uu.net =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- End of Responses Michael A. Peterson ipmp500@indyvax.iupui.edu IUPUI Dept. of Chemistry From rsjuds@snll-arpagw.llnl.gov Thu Nov 19 05:17:18 1992 Date: Thu, 19 Nov 92 13:17:18 -0800 From: rsjuds@snll-arpagw.llnl.gov (judson richard s) Message-Id: <9211192117.AA22523@snll-arpagw.llnl.gov> To: chemistry@ccl.net Subject: Water Potentials I'm running some simulations of small molecules in water where it is important to have the diffusion coefficient of the water modelled as accurately as possible. Can someone tell me whether there are any water potentials that have this property, or at least which ones come closest? ----------------------------------------------- | Richard Judson | | Center for Computational Engineering | | Sandia National Laboratories | | Livermore, CA 94551-0969 | | email: rsjuds@sandia.llnl.gov | ----------------------------------------------- From mwilson@max.arc.nasa.gov Thu Nov 19 07:50:28 1992 Date: Thu, 19 Nov 92 15:50:28 -0800 From: mwilson@max.arc.nasa.gov (Michael A. Wilson) Message-Id: <9211192350.AA12563@max.arc.nasa.gov> To: chemistry@ccl.net Subject: gnuplot on SGI I sent mail to the person who posted the summary of WordProcessing and graphics on SGI's as well as to the original poster, who suggested that I should post this to the list: In the summary, it was mentioned that gnuplot would not compile on an SGI without gcc. This is not correct. We have compiled gnuplot versions 2.x and 3.0 on SGI's under IRIX 3.2, 3.3.x and 4.0.x using the standard C compiler development system. Some changes may have been necessary in the Makefile compiler options, but no source code mods were necessary... Mike _____________________________________________________________________________ Mike Wilson, MS 239-4 mwilson@max.arc.nasa.gov (415) 604-5759 day NASA Ames Research Center (415) 604-1088 fax Moffett Field, CA 94035 (510) 523-7790 eve From chemistry-request@ccl.net Thu Nov 19 19:13:02 1992 Date: 17 Nov 1992 17:07:58 -0600 (CST) From: CHEM86@Jetson.UH.EDU Subject: Programs to ease Normal Coordinate Analysis To: chemistry@ccl.net Message-Id: <01GR9KH6NPRM8ZFBI8@Jetson.UH.EDU> Dear Netters, Some time ago I wrote two short FORTRAN programs: RANKZ and RANKFG. They can serve as handy tools for dealing with the normal coordinate analysis (NCA) using the GF-matrix Wilson method. To my knowledge, NCA is most commonly done by running well-known 1963 Schachtschneider & Mortimer programs (or their modifications). The basic idea is still the same: 1) Generate inverse of the kinetic energy matrix G 2) Generate the force constant matrix F_ij = sum_k (Z_ijk*f_k) (where f_k denotes the set of independent force constants, Z_ijk is the so-called Z-matrix which combines f_k 's to give F-matrix) [NOTE: - please, do not confuse the NCA Z-matrix with the "ab initio" Z-matrix (providing molecular geometry in internal coordinates) !!!] 3) Symmetrize matrices G and F (via Z) 4) Solve GF secular equation to obtain frequencies and normal eigenvectors. Generating good input for large molecules is still an art rather than routine, especially for beginners (like me). It is not easy to define sufficiently good set of internal coordinates and independent force constants. Moreover, globally independent force constants may become dependent within one symmetry block (after symmetrization of G and Z matrices). RANKZ and RANKFG programs test how good is the NCA input. RANKZ calculates rank of the combined Z-matrix (one or several combined symmetry blocks or unsymmetrized) using Gauss elimination. The input file(s) (with extension .ZMAT --- though it may be changed if needed) contain(s) the non-zero elements of Z-matrix in format (3I3,F9.6). The input is terminated by a sequence -1 0 0 0.000000. User can combine several blocks of symmetrized Z-matrix, each in separate '*.ZMAT' file, by answering 'N' when program asks 'END OF DATA ?' . The output file (extension '*.RAOUT') produced by the program contains a list of offending force constants which are either dependent or missing. RANKFG uses singular value decomposition to calculate the rank of the real symmetric matrix. It can be therefore used to test either G or F matrices. The rank of these matrices tells the number of frequencies from NCA calculations which will result in reasonable values within each of the symmetry blocks (this number depends on the redundancy of internal coordinates). The number can be then compared with the group-theoretical value. To calculate the rank of the G-matrix (or its symmetry block) the user should input '0' as a 'number of force constants'. The input file in this case should have an extension '*.GMAT' and should contain non-zero elements of G-matrix in the format (2I3,F12.6). The terminating sequence which markes the end of the list is -1 0 0.000000. The output produced by the program consists of the rank and the singular values of G-matrix (file *.RAOUTG). To calculate rank of F-matrix (or its symmetry block) user should input: the actual number of force constants, specify corresponding Z-matrix input file (*.ZMAT), and specify the file containing force constants (extension *.FI). The F-matrix is then calculated by the program. The format of Z-matrix file is the same as that of RANKZ input file. The force constant file *.FI has a free input format. In the output program gives the rank of the F-matrix and its singular values (file *.RAOUTF). Please, report bugs to chem86@jetson.uh.edu (Robert Fraczkiewicz) --- The programs and examples are available from Computational Chemistry List archives on www.ccl.net in directory pub/chemistry/normal_coor_anal. The files are: This file: readme Source code of the RANKZ program: rankz.f Source code of the RANKFG program: rankfg.f Examples of input files for some 60-atom molecule: (One symmetry block A2G, dimension=20, number of force constants=99) Z-matrix input file : a2g.zmat G-matrix input file : a2g.gmat Force constant file : a2g.fi Examples of output files: RANKZ output : a2g.raout RANKFG outputs : a2g.raoutg and a2g.raoutf You can retrieve the programs and examples via ftp as: ftp www.ccl.net (or ftp 128.146.36.48) Login: anonymous Password: your_email_address ftp> cd /pub/chemistry/normal_coor_anal ftp> ascii ftp> prompt (to skip yes/no prompts for individual files) ftp> mget * ftp> quit If you do not have ftp, you can retrieve files via e-mail interface by sending a message: --------- cut here start ----- send ./normal_coor_anal/a2g.fi from chemistry send ./normal_coor_anal/a2g.gmat from chemistry send ./normal_coor_anal/a2g.raout from chemistry send ./normal_coor_anal/a2g.raoutf from chemistry send ./normal_coor_anal/a2g.raoutg from chemistry send ./normal_coor_anal/a2g.zmat from chemistry send ./normal_coor_anal/rankfg.f from chemistry send ./normal_coor_anal/rankz.f from chemistry send ./normal_coor_anal/readme from chemistry -------- cut here end -------- to OSCPOST@ccl.net or OSCPOST@OHSTPY.BITNET. Robert Fraczkiewicz Department of Chemistry University of Houston CHEM86@jetson.uh.edu --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everyone CHEMISTRY-REQUEST@ccl.net --- coordinator OSCPOST@ccl.net send help from chemistry Anon. ftp www.ccl.net ---