From chemistry-request@server.ccl.net Tue Jul 6 10:14:28 1999 Received: from lipid.biocomp.unibo.it (ivan@lipid.biocomp.unibo.it [137.204.193.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA31798 for ; Tue, 6 Jul 1999 10:14:26 -0400 Received: from localhost (ivan@localhost) by lipid.biocomp.unibo.it (8.8.7/8.8.7) with ESMTP id QAA07469 for ; Tue, 6 Jul 1999 16:11:40 +0200 Date: Tue, 6 Jul 1999 16:11:40 +0200 (CEST) From: Ivan Rossi To: CompChem Mailing List Subject: School on proteomics Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII BOSS'99 - 2nd BOLOGNA SUMMER SCHOOL on Biotechnology PROTEIN SEQUENCE ANALYSIS IN THE GENOMIC ERA 10-16 October 1999 - Bologna (Italy) Main topics will be: data mining and retrieval, protein sequence analysis, protein structure prediction and functional genomics. Round table discussions will focus on "hot" topics of proteomics at the end of the millenium. TEACHERS: Miguel A. Andrade - EMBL, Heidelberg DE Rolf Apweiler - EBI, Hinxton UK Pierre Baldi - Net-ID, Caltech, Pasadena USA Geoff Barton - EBI, Hinxton UK Soren Brunak - Technical University of Denmark, Lyngby DK Georg Casari - LION bioscience AG, Heidelberg DE Rita Casadio - CIRB, Bologna IT Mario Compiani - CIRB, Bologna IT Piero Fariselli - CIRB, Bologna IT David Jones - University of Warwick, Coventry UK Beate Marx - EBI, Hinxton UK Burkhard Rost - Columbia University, New York USA Michael Sternberg - Imperial Cancer Research Fund, London UK APPLICATION should be submitted by e-mail to: e-mail: school@biocomp.unibo.it You will be notified by e-mail of acceptance. Maximum number of partecipants is limited to 30 students. Deadline for application is August 20/1999 Registration will be payed upon acceptance with modalities to be specified. More information can be found on the BOSS99 Web page at: http://www.biocomp.unibo.it/school SCHOOL CHAIRS: L. Masotti (CIRB) and R. Casadio (CIRB) Scientific Committee: R. Apweiler, S. Brunak, B. Rost, R. Casadio, A. Valencia Organizing Committee: M. Compiani (CIRB), P. Fariselli (CIRB), E. Rossi (CINECA), G Maino (ENEA) Local Committee: PL. Martelli (CIRB), I. Jacoboni (CIRB), I. Rossi (CIRB). ORGANIZING SECRETARY CIRB - c/o Dept. of Biology, University of Bologna via Irnerio 42, I-40126 Bologna (Italy) tel: (+39) 051 354005 fax: (+39) 051 242576 e-mail: school@biocomp.unibo.it -- Dr. Ivan Rossi - CIRB Biocomputing Unit e-mail: ivan@biocomp.unibo.it Web: http://www.biocomp.unibo.it/ivan From chemistry-request@server.ccl.net Mon Jul 5 23:51:54 1999 Received: from gatekeeper.mahindrabt.com ([202.54.20.162]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA26523 for ; Mon, 5 Jul 1999 23:51:46 -0400 Received: (from uucp@localhost) by gatekeeper.mahindrabt.com (8.9.3/8.8.6) id JAA24314 for ; Tue, 6 Jul 1999 09:16:39 +0530 Received: from intranet.pune.mahindrabt.com(202.41.13.243) via SMTP by gatekeeper1.mahindrabt.com, id smtpda24309; Tue Jul 6 09:16:34 1999 Received: from mahindrabt.com ([10.4.8.191]) by intranet.pune.mahindrabt.com (8.8.7/8.8.7) with ESMTP id JAA17893 for ; Tue, 6 Jul 1999 09:16:00 +0530 Message-ID: <37817A27.78B3668@mahindrabt.com> Date: Tue, 06 Jul 1999 09:08:16 +0530 From: "Dr. Sudhir A. Kulkarni" Organization: Mahindra British Telecom Limited X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Tinker problems Content-Type: multipart/mixed; boundary="------------5DA7C54D6B307F601411E57C" This is a multi-part message in MIME format. --------------5DA7C54D6B307F601411E57C Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, I am a new user of Tinker program and trying to get optimized structure of test molecule Triglycine (NH2-CH2-CO-NH-CH2-CO-NH-CH2-COOH) with different force fields available with the program. Unfortunately, I was successful only with MM2 force field. For all other FF, there was either some of the bond angle or torsional parameter said to be undefined. Can any one suggest, what is a way out for this problem? Another question is : how all MM programs in commercial softwares get parameters for all types of bonding? (Atleast they don't terminate saying --- parameter not found!). Thanks in advance. Sudhir Kulkarni --------------5DA7C54D6B307F601411E57C Content-Type: text/x-vcard; charset=us-ascii; name="sudhirk.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Dr. Sudhir A. Kulkarni Content-Disposition: attachment; filename="sudhirk.vcf" begin:vcard n:Kulkarni;Dr. Sudhir A. x-mozilla-html:FALSE org:Mahindra British Telecom Limited version:2.1 email;internet:sudhirk@MahindraBT.com x-mozilla-cpt:;0 fn:Dr. Sudhir A. Kulkarni end:vcard --------------5DA7C54D6B307F601411E57C-- From chemistry-request@server.ccl.net Tue Jul 6 07:25:09 1999 Received: from theo1.theochem.tu-muenchen.de (theo2.theochem.tu-muenchen.de [129.187.191.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id HAA30314 for ; Tue, 6 Jul 1999 07:24:59 -0400 Received: from theo350.theochem.tu-muenchen.de (theo350.theochem.tu-muenchen.de [129.187.157.44]) by theo1.theochem.tu-muenchen.de (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id NAA07497 for <@theo1.theochem.tu-muenchen.de:chemistry@ccl.net>; Tue, 6 Jul 1999 13:19:56 +0200 Received: (from gisdakis@localhost) by theo350.theochem.tu-muenchen.de (950413.SGI.8.6.12/950213.SGI.AUTOCF) id NAA07516 for chemistry@ccl.net; Tue, 6 Jul 1999 13:19:56 +0200 From: "Philip Gisdakis" Message-Id: <9907061319.ZM7514@theo350.theochem.tu-muenchen.de> Date: Tue, 6 Jul 1999 13:19:55 -0600 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@ccl.net Subject: Summary: Orbital Viewer Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Collegues, here is the summary of my question concerning Gaussian orbital viewers for Windows NT. We need such a tool for our Quantum Chemistry Laboratory. This is a course about quantum chemistry in the internet. If you're interested please visit our web-page: http://qcl.theochem.tu-muenchen.de/ Thanks to all who replied. Philip ---------------------------------------------------------- Original question: Dear Collegues, we are seeking for are free orbital viewer for Windows NT, which can display MOs calculated by Gaussian. We need it for educational purposes. Also suitable would be a program, which can build a VRML file, as molden does, but in command line mode. We would run that program on our Unix Server and the VRML-file is just transferred to the students PC, which will display it. Thanks in advance Philip ---------------------------------------------------------- Answer 1 (Martin Leboeuf): Hallo ! Fuer Unix, schlag ich Ihn VU vor : http://www.cerca.umontreal.ca/vu/ VU kann VRML schreiben. Fuer Chemie Beispiele : http://www.cerca.umontreal.ca/~leboeuf/Vu/ Gruss, Martin. ---------------------------------------------------------- Answer 2 (Wolf-Dietrich Ihlenfeldt): Haben Sie schon einmal einen Blick auf OrbVis http://www2.ccc.uni-erlangen.de/services/orbital/index.html geworfen? Wir benutzen als QM-Programm VAMP, aber eine Anpassung an Gaussian ist sicher nicht unmoeglich. ---------------------------------------------------------- Answer 3 (Jose I. Garcia): Dear Philip, Here are several possibilities: * GOpenMol (http://laaksonen.csc.fi/gopenmol/gopenmol.html). It runs under Windows 95/98/NT, and it is able to display nice images of gaussian cube files, and hence of M.O. also. It is my favorite for M.O. display, but it is not able to export images to VRML files. * Molden (http://www.caos.kun.nl/~schaft/molden/molden.html) It runs mainly on Unix machines, but the last version can also run on Windows 95/NT machines (however, it requires a X-Windows Server software installed to run; see the Molden page for details) * Chem3D Ultra (from Cambridge Software). This is commercial soft, but not expensive for educational purposes. It is able to display gaussian cube files, but it do not export to VRML files. I hope this helps you. Regards. Jose I. Garcia ---------------------------------------------------------- Answer 4 (Max Valdez): Hi Philip: I think molden is the only good and FREE program that can do that, and as i can understand, you don't have graphic terminal i recomend you to put at least one xterm emulator, as you need to see the orbital before building a VRML file of it, or you will never be sure of what image correspond to a given density value. there is one free xterm emulator in http://www.microimages.com/ and there are some commercial emulator that work better if you want to spend some money. Best Regards Max ---------------------------------------------------------- Answer 5 (Jose Conceicao): Hi Philip Here is an email message I received from other workers using Gaussian 98W (windows version) about viewers. Hope it works for you. J.Conceicao > Dear Colleague: > My group has lately been doing quantum chemistry and MD calculations > to aid experimental interpretation. We needed a good visualization > program, and wanted one that would run on PCs because that's what we > have. Leif Laaksonen (http://laaksonen.csc.fi/gopenmol/gopenmol.html) > has written a powerful (and free) program called gOpenMol that runs on > Win 95/98/NT boxes, as well as Unix workstations. The program can > work with about 20 common input formats (Gaussian, GAMESS, Mopac, > Xmol, PDB, ....). gOpenMol does lots of things, and makes very well > rendered images/animations that can be exported in a variety of > formats. It uses Tcl scripts, so it is possible to automate or extend > the program to suit your application. > One problem has been that documentation is minimal, and to help with > this, I have written a tutorial that covers the basics of gOpenMol. > This can be viewed or downloaded by clicking the "Using gOpenMol" > button at the bottom of my web page: > http://www.chem.utah.edu/chemistry/faculty/anderson/anderson.html > The tutorial demonstrates the following operations: > Visualize molecular structures in all the usual formats (stick, ball > and stick....) > Visualize MOs, densities, spin densities, etc, in a variety of formats > (contours, surface plots...) > Animate vibrations from a quantum chemistry calculation, and write out > animations as frames or movies. > Visually manipulate subgroups of atoms (e.g. subunits in a complex) > then write out geometries for further calculations (e.g. to generate > guesses for transition state geometries). > gOpenMol can do many other things, but this should get you started. > > Prof. Scott L. Anderson anderson@chemistry.utah.edu > Chemistry Department Ph:(801)585-7289 > University of Utah FAX:(801)581-8433 > 315 S. 1400 E. RM Dock > Salt Lake City, UT 84112-0850 > http://www.chem.utah.edu/chemistry/faculty/anderson/anderson.html ---------------------------------------------------------- Answer 6 (Leif Laaksonen): Philip, Please have a look at gOpenMol at: http://laaksonen.csc.fi/gopenmol/ I'm working on a VRML filter, which will be included in the next release. Regards, -leif laaksonen ---------------------------------------------------------- Answer 7 (Serge Pissarev): Molden for Windows NT can export the orbitals into VRML. It uses X-server to perform drawing. Updated version can import the Gaussian wavefunctions. I do not know others that *DO NOT* use X-server. If you do know them, particularly the ones that could operate with both Gussian and GAMESS-US wavefunction, please, let me know (summarize in CCL?) ---------------------------------------------------------- Answer 8 (Gijs Schaftenaar): Dear Philip, Molden can run VRML in the commandline mode: molden -V vrmlfile commandfile commandfile: some title file=gaussain.log space=0.1 vrml2.0 (you could use vrml as keywor to specify vrml1.0) There is a molden vrml orbital/density service on our web site that uses this setup (URL: http://www.caos.kun.nl/~schaft/molden/moldenservice.html) Secondly, there is a Windows95/NT version of molden, it needs a Xwindows emulator like xwin32 to run. Have a look at URL: http://www.caos.kun.nl/~schaft/molden/windowsnt95.html PS: be sure to download both zip files: ftp://ftp.caos.kun.nl/pub/molgraph/molden/bin/molden_windows_nt_95.zip ftp://ftp.caos.kun.nl/pub/molgraph/molden/bin/molden_windows_nt_95_update.zip The molden home page is at: html://www.caos.kun.nl/~schaft/molden/molden.html Best Regards, Gijs Schaftenaar ---------------------------------------------------------- Answer 9 (Alexander Klinsky): Why dont you use Molden for Windows NT? I have been upgrading recently my port on the official molden server from Gjs Shaftenar to the latest 3.5 version from second June 1999. ---------------------------------------------------------- -- Philip Gisdakis o-----------------------------------------------------------------o / Philip Gisdakis gisdakis@theochem.tu-muenchen.de / \ / Theoretical Chemistry Phone: +49 +89 289 13618 (Univ.) / o /Technische Universitaet Muenchen 67908232 (Privat) / / / Lichtenbergstrasse 4 / / / D - 85747 Garching / / o-----------------------------------------------------------------o / \ \ / o-----------------------------------------------------------------o From chemistry-request@server.ccl.net Tue Jul 6 09:25:44 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA31316 for ; Tue, 6 Jul 1999 09:25:38 -0400 Received: from email.nist.gov (email.nist.gov [129.6.2.7]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id JAA23476 for ; Tue, 6 Jul 1999 09:20:36 -0400 (EDT) Received: from feldmann.nist.gov (feldmann.nist.gov [129.6.178.78]) by email.nist.gov (8.9.3/8.9.3) with ESMTP id JAA23948; Tue, 6 Jul 1999 09:17:10 -0400 (EDT) Received: from localhost (chem@localhost) by feldmann.nist.gov (8.8.8+Sun/8.8.8) with SMTP id JAA04438; Tue, 6 Jul 1999 09:04:51 -0400 (EDT) Date: Tue, 6 Jul 1999 09:04:51 -0400 (EDT) From: Steve Heller To: lists , amber@cgl.ucsf.edu, APPLSPEC@listserv.uga.edu, cache@pacificu.edu, CHEMCHAT@UAFSYSB.UARK.EDU, CHEME-L@ULKYVM.LOUISVILLE.EDU, CHEMED-L@atlantis.UWF.EDU, CHEMIG@LIST.NIH.GOV, CHEMISTRY@www.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, ICS-L@UMDD.UMD.EDU, isisforum-l@mdli.com, ISOGEOCHEM@LIST.UVM.EDU, listproc@msi.com Subject: ChemInt'99 - Complete program now available Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The complete program of all lectures and contributed talks for the Chemistry & the Internet meeting is now available. The web site is also now keyword searchable. All of the ChemInt'98 presentations on the web site can be searched. Go to: www.chemint.org This note is to also a reminder that the deadline for poster abstracts submissions for presentations at the ChemInt'99 meeting is September 1. The Chemistry and the Internet (ChemInt'99) meeting being held in at Georgetown University in Washington DC on September 25-27, 1999. The program of invited speakers and panel members of the 3 panel sessions is available on the meeting web site - www.chemint.org You are urged to look at the program and to consider submitting a poster paper to the meeting. The main lecturers for the meeting will be: Alan Arnold, University College (UNSW) Steven Bachrach, Northern Illinois University Robert Bovenschulte, ACS Stephen Boyer, IBM Karl Harrison, Oxford University Clemens Jochum, Deutsche Bank Gary Mallard, NIST Tom Pierce, Rohm & Haas Jerome Reichman, Vanderbilt Achim Zielesny, Bayer AG Steven S. Zumdahl, University of Illinois at Urbana-Champaign The (current) corporate sponsors for the meeting are: ChemWeb and the Internet Journal of Chemistry (IJC) Technical Sponsors are: ACS CINF Division ACS COMP Division The Chemical Structure Association (CSA) Georgetown University - Department of Chemistry International Union of Pure and Applied Chemistry (IUPAC) (pending) Japan Association for International Chemical Information (JAICI) Special Libraries Association (SLA) Chemistry Division Royal Society of Chemistry (RSC) Steve Heller Steve Heller, Guest Researcher NIST/SRD, Mail Stop: 820/113 820 Diamond Avenue, Room 101 Gaithersburg, MD 20899-2310 USA E-mail: srheller@nist.gov *** Details on how to be removed from this list as well as an *** *** archive of recent postings are available at *** *** http://www.rcsb.org/pdb/forum.html *** From chemistry-request@server.ccl.net Tue Jul 6 14:18:08 1999 Received: from darkwing.uoregon.edu (genghis@darkwing.uoregon.edu [128.223.142.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA01694 for ; Tue, 6 Jul 1999 14:18:07 -0400 Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.9.3/8.9.3) with SMTP id LAA10797 for ; Tue, 6 Jul 1999 11:13:05 -0700 (PDT) Date: Tue, 6 Jul 1999 11:13:05 -0700 (PDT) From: "Dale A. Braden" To: cclpost Subject: Summary: MO contour plots Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, This is the summary of responses to my question about programs which can plot MO contours using a Gaussian .cub or .fchk file. Thank you to all who responded. In short, there aren't any such programs yet. This is amazing, given the importance of simple, black and white printouts suitable for publication. This functionality will likely be included in future versions of some programs, but apparently isn't available just yet. One must at the very least write code of some kind to take a slice through the cube data. (If someone has such a routine already written, perhaps it could be made available in the CCL software archives?) If one runs a Gaussian job with the appropriate keywords to begin with, then Gopenmol can use the information in the .log file to plot black and white contours. Best wishes to all, Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu From chemistry-request@server.ccl.net Tue Jul 6 15:16:46 1999 Received: from darkwing.uoregon.edu (genghis@darkwing.uoregon.edu [128.223.142.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA02579 for ; Tue, 6 Jul 1999 15:16:45 -0400 Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.9.3/8.9.3) with SMTP id MAA04489 for ; Tue, 6 Jul 1999 12:11:43 -0700 (PDT) Date: Tue, 6 Jul 1999 12:11:42 -0700 (PDT) From: "Dale A. Braden" To: cclpost Subject: Summary: MO contour correction! Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, I made a mistake in saying that, with appropriate keywords, Gaussian will generate a logfile suitable for use by Gopenmol to produce MO contour plots. It is Molden that can use such output. My apologies! I've also looked into writing a little unix script to take a slice from a Gaussian cube file and formatting the resulting data for gnuplot. This shouldn't be too difficult, but it occurred to me that the molecular geometry won't be visible with the contours. Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu