From dju@merck.com Fri Aug 6 04:24:40 1993 Message-Id: <199308101305.AA10960@oscsunb.ccl.net> From: dju@merck.com Subject: call for papers (ACS March 1994) To: CHEMISTRY@ccl.net Date: Fri, 6 Aug 1993 09:24:40 -0500 (EDT) CALL FOR PAPERS CALL FOR PAPERS The American Chemical Society, Computers in Chemistry Division is sponsoring a symposium on: G PROTEIN COUPLED RECEPTORS: STRUCTURE AND MODELING at the San Diego Meeting March 13-18, 1994. The theme of the ACS Meeting is Aquatic Chemistry, Biotechnology and Molecular Modeling in Chemistry. This is the first call for papers. If you are interested in presenting a paper on this topic please respond preferably by Email by September 7th, 1993. Please enclose a short (150 words) abstract. Dennis J. Underwood Merck Research Laboratories PO Box 2000 Rahway NJ 07065-0900 (908) 594 7221 voice (908) 594 4224 FAX dju@merck.com Email From nauss@ucmodl.che.uc.EDU Tue Aug 10 06:45:03 1993 Date: Tue, 10 Aug 1993 10:45:03 -0400 From: nauss@ucmodl.che.uc.EDU (Jeffrey L. Nauss) Subject: Discover users in Ohio To: CHEMISTRY@ccl.net Message-Id: <9308101445.AA05940@ucmodl.che.uc.edu> I would like to know who are users of Discover in the State of Ohio and who also would be willing to lend their support to the upgrade of the current Discover software at the Ohio Supercomputer Center. The version there is quite old and will be deleted shortly. We here at the University of Cincinnati are heavy Discover users and would like to see Discover maintained at OSC and upgraded to a current version. But we need support from elsewhere in the state. Thanks for your time and interest. Jeff Nauss **************************************************************************** * Dr. Jeffrey L. Nauss * telephone: 513-556-0148 or 9200 * * Director, Molecular Modeling Services * Fax: 513-556-9239 * * Department of Chemistry * * * University of Cincinnati * e-mail: nauss@ucmodl.che.uc.edu * * Cincinnati, OH 45221-0172 * or nauss@ucchem.oa.uc.edu * **************************************************************************** From cory@riemann.math.mun.ca Tue Aug 10 09:28:39 1993 Date: Tue, 10 Aug 1993 11:58:39 -0230 From: "Cory C. Pye" Message-Id: <9308101428.AA27601@riemann.math.mun.ca> To: chemistry@ccl.net Subject: Summary: Plotting Molecular Orbitals Subject: Plotting ab initio molecular orbitals Here is a summary of responses as promised. **********************Original Inquiry - Me****************************** Hello fellow netters, I am looking for a program which can plot molecular orbitals, given a geometry, basis set, and final SCF coefficients. My requirements are 1) Preferably SGI Indigo with output to either the screen or printer (postscript, dvi). Alternatives: VAX 4500, Apollo DN10000, (VIC-20 :-)) 2) Ability to use any basis set given to it. (Not absolutely necessary) 3) Ability to use any atom defined within the basis set. (necessary) 4) Hopefully, public domain or shareware (I'm a grad student => $ = 0) 5) Easy to install. 6) Ab initio data (DFT & semiemp. would be an interesting bonus) 7) geometry: Cartesian or z-matrix(preferred) I am thinking along the lines of the program PSI/88 which I have found very useful. The code, however is heavily optimized and probably difficult to extend to arbitrary bases and atoms. It can handle atoms H-Ar and bases STO-3G, 3-21G, 6-31G with and without diffuse and polarization functions. I have used this on a VAX 4500. There is a program xpsi of which I am aware (basically the above with application of f2c and using PEX libraries) if I am not mistaken. Alternatively, somebody could tell me the status of PEX on the SGI, and if free, an ftp site where one could obtain this. This of course does not solve my problem of wishing to print molecules with atoms larger than Ar. I suspect that there may be some Explorer modules or some extension of programs like xmol which may be able to do this. Remember, free is the key word. I do not want to envision the idea of writing it myself, except as a last resort, since I program in OSIPE-Fortran ('Fortran++') and I would probably have to learn C (C++) to take advantage of the full capabilities of X/Motif, GL, or PEX. Please send replies to cory@riemann.math.mun.ca (as in header) or if this fails try cory@kean.ucs.mun.ca cory@morgan.ucs,mun.ca cory@zeus.chem.mun.ca cory@bohr.chem.mun.ca I will try to post a summary. *************************Responses to my query*********************** In no particular order: (with some minor editing) Note: I have used <> to insert my comments. EXPLORER --------------------------------------------------------------------- From: jjv5@retina.chem.psu.edu (Jim Vincent) (Dr. ?) Omer Casher has developed Explorer modules for doing lots of stuff with Gaussian and Mopac output. He said he will probably be putting them in the public domain. Details will be posted to comp.graphics.explorer in about two weeks. He will be showing the modules at SIGGRAPH in California. You might want to just check in on that group in a while. I will be gettin the modules as soon as they become available. If you like I can tell you more about what they do after I use them a little. Jim Vincent jjv5@retina.chem.psu.edu SciAn --------------------------------------------------------------------- From: vazquez@iqm.unicamp.br (Pedro A M Vazquez) Hello: Take a look the SciAn package from fsu. I'm sending to you the README file from where you can get more info. guada@iqm.unicamp.br has done some little programs to interface SciAn to mopac and g92 outputs. Regards Pedro [ README file from SciAn deleted:] Some highlights kept: SciAn currently runs on two platforms: 1) Silicon Graphics 4D workstations 2) IBM RISC/System 6000 workstations SciAn will run only on IBM RISC/System 6000 workstations that have 3-D graphics accelerators that provide GL compatibility. SciAn also requires a Z-buffer. If you would like to obtain SciAn, please send electronic mail to scian-info@scri.fsu.edu, if you haven't already done so. You can also request to be put on the SciAn mailing list, which will keep you informed of updates. SciAn is normally distributed via anonymous ftp from ftp.scri.fsu.edu. If you do not have access to anonymous ftp, send us mail, and we'll try to figure out some other way to get you the program. It is much easier to get the program through ftp, however, and it's certainly easier to get updates that way. The SciAn program and documentation are located in the SciAn subdirectory of the pub directory. To get into that directory, enter cd pub/SciAn In that directory, you will find a README file (which is this document ) and several subdirectories. The release subdirectory contains the release versions of SciAn. Obtaining SciAn from this directory is described in section 3.2. (stuff deleted) The documentation subdirectory contains documentation for SciAn. Obtaining and printing it is described in section 3.3. In the "release" subdirectory (enter cd release to get to the directory) you will find several files. They will all have names of the form scianXXX.tar.Z, where XXX is the version number of SciAn. For example, the file scian060.tar.Z contains SciAn version 0.60. PLTORB ----------------------------------------------------------------------- From: "System Manager, and VAX Gopher" You didn't specify which package you're using to obtain the input for the plotting program, but there is a package PLTORB that is distributed with GAMESS that may do what you want. It can be used with GaussianXX output, providing you can get Gaussian to choke out the data in an ascii format. GAMESS will punch an input deck for it. The program only does Contour plots, not 3d. I've read the code in PSI/88, and while I haven't taken action on it yet (I too am a grad student, and have a minimal amount of time to spend on side projects at this point), the code seems easy to extend to arbitrary bases. The simplest action would be to add code for the specific basis sets you're using. Finally, QCPE has some older programs that may be modifiable, in the sense that if you write a new graphics interface to them, the core plotting routines are already present. -fred MOPLOT 2.0 ----------------------------------------------------------------------- Message 1: From: DLICHTEN@CCIT.ARIZONA.EDU I have developed a series of programs that come very close to your request. They allow virtually any Gaussian or Slater basis set and any vector coefficients, with alterations of the density matrix, etc. if you so desire. The original program MOPLOT was written in 1970 and only allowed single plane plots. This program has been available from QCPE for many years. The new MOPLOT version 2.0 does three dimensional grids as well. The output can be sent through the plotting routines of PSI88 if desired, or plotted with routines that are provided. Right now the graphics is a choice of hewlett-packard, tectronix or VGA for the PC. It is easy to incorporate other graphics. All the programs are in fortran 77 and run on both unix and vax systems without alteration. The disadvantage is that the code is probably not designed for ease of use with your wavefunctions, and you may want to alter the Gaussian subroutine to read in your wavefunctions more easily. I would be interested in having other users extend the code for their applications. If you are interested I will make the code available on a FTP site. Dennis L. Lichtenberger Professor of Chemistry Department of Chemistry University of Arizona Tucson, AZ 85721 unnamed -------------------------------------------------------------------------- From: "Terry R. Coley" I have something that will do this. It runs on a Silicon graphics and creates output suitable for viewing in AVS. It is currently difficult to install and maintain, however. I am in the process of cleaning it up. In a few months I will make it freely available. Check with me after a few months if you are still interested and I'll give you a status update. - Terry | Parallelograms terry@wag.caltech.edu 818-395-2723 | PO Box AA Caltech, M/S 139-74 | Pasadena, CA 91102 Pasadena, CA 91125 | 818-577-5515 Voice/FAX ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ In addition, I received a couple of requests. If I have omitted anyboby, then please e-mail and I will add your suggestions to this file and repost in a few weeks. At this point I would like to thank everybody who responded. I am in the process of obtaining some of the software. I will share with anybody my experiences with the application of the software to problems in the 'real' world, via private e-mail. If enough are interested, I may present a critical review of software if the respective authors allow this. (Provided I have time, of course) -Cory Pye From Jonathan.Connor@mailhost.manchester-computing-centre.ac.uk Tue Aug 10 17:21:04 1993 Message-Id: <199308101629.AA13910@oscsunb.ccl.net> Subject: meeting To: Chemistry Date: Tue, 10 Aug 93 17:28:29 BST From: Jonathan Connor Forwarded message: X-Version: Mailbase (TM) Enhanced List Manager Version 2.3 Date: Mon, 9 Aug 93 11:00:41 BST Message-Id: <2002.9308091000@dir.mcc.ac.uk> To: chest-embase@mailbase.ac.uk From: awhit@dir.mcc.ac.uk X-List: chest-embase@uk.ac.mailbase Reply-To: awhit@dir.mcc.ac.uk Sender: chest-embase-request@mailbase.ac.uk Precedence: list UNIVERSITY OF MANCHESTER UMIST MANCHESTER COMPUTING CENTRE *********************************************** * INTERNATIONAL CONFERENCE * * * * for * * * * CHEMICAL INFORMATION USERS * * * * * * PRESENT SITUATION AND FUTURE DEVELOPMEN Tuesday 30 November - Wednesday 1 December 1993 MANCHESTER, UK The purpose of the Conference is to address the needs of users of chemical information from both the academic and industrial sectors. It will provide an opportunity for users to meet with other users, researchers and information providers in order to exchange views and to discuss problems, with the aim of influencing future provision of chemical information. The Conference which is to be chaired by Dr Diana M Leitch (University of Manchester) comprises of five sessions. PROGRAMME OUTLINE Session 1 - Needs of the Chemist: Key Requirements and Expectations from Database Suppliers; Overview of Current Chemical Information Systems; Problem Areas. Session 2 - New Developments: SuperJANET; Daresbury-Enhanced Service; Beilstein-The Future; Demonstrations. Session 3 - Meeting the Needs: Chemical Abstracts Service; Royal Society of Chemistry and STN International; Derwent Publications Ltd; Molecular Design Ltd; Chemical Design Ltd; BIDS & CHEST. Session 4 - Ongoing Projects and Research: Overview; Internet Facilities; Document Delivery; The Learning Process. Session 5 - The Way Forward: Interactive Discussion led by a Panel of Speakers KEY SPEAKERS Speakers who have already agreed to contribute are: Professor Sir Geoffrey Allen, F.Eng FRS (Kobe Steel Ltd); Professor K R Jennings (University of Warwick); Dr J Barnard (Barnard Chemical Information Ltd); Dr W T Hewitt (Manchester Computing Centre); Professor A J Lawson (Beilstein Institute, Frankfurt-am-Main); Ms H Schofield (UMIST); Dr J H Scrivens (ICI Chemicals and Polymers); Professor J M Thornton (University College, London); Dr Joint organisers Dr J M Bruce (Chemistry Department, University of Manchester), Dr Diana M Leitch (John Rylands University Library of Manchester), Dr A F Neville (John Rylands University Library of Manchester), Ms H Schofield (Joule Library, UMIST), Mr R J Stephenson (Manchester Computing Centre), Dr A Whiting (Chemistry Department, UMIST). Further details and application forms from Dr M P Coward (Conference Secretary) Chemistry Department, UMIST, PO Box 88, Manchester M60 1QD, UK Tel 061 200 4491, Fax 061 228 1250 Email M.P.Coward@umist.ac.uk If you are interested in receiving further details, please fill in and send the following: Surname . . . . . . . . . . . . . . . . . . . . . . . . . . First Name . . . . . . . . . . . . . . . . . . . . . . . . Company or Institution . . . . . . . . . . . . . . . . . . Address . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Post (Zip) Code . . . . . . . Telephone . . . . . . . . . . Telefax . . . . . . . . . . . Email . . . . . . . . . . . . . . . . . . . . . . . . . . . END OF MESSAGE -- Professor J.N.L. Connor, Phone(direct line): 061-275-4693 (national) Department of Chemistry, :+44-61-275-4693 (international) University of Manchester, Manchester M13 9PL, Phone(secretary): 061-275-4686 or 4600 England. Fax: 061-275-4598 From melkor!vx1105.dnet!drapeau@uunet.UU.NET Tue Aug 10 03:48:48 1993 Message-Id: <9308102225.AA23071@relay1.UU.NET> Date: Tue, 10 Aug 93 08:48:48 -0500 From: melkor!vx1105.dnet!drapeau@uunet.uu.net To: uunet!chemistry%ccl.net@uunet.uu.net Subject: Refractive Index Estimates Greetings Fellow Netters, Can anyone give reference to an algoritm or software for estimating simple organic compound indices of refraction as a function of wavelength? I will gladly summarize responses to the net. | rjd@adc.com ADC Telecommunications, Inc. | | 4900 W. 78th Street | | Minneapolis, MN 55435, USA |