From owner-chemistry@ccl.net Fri Jan 26 09:02:43 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id JAA13531; Fri, 26 Jan 1996 09:02:42 -0500 Received: from ocserv.chemie.uni-hamburg.de for brock@chemie.uni-hamburg.de by bedrock.ccl.net (8.7.1/950822.1) id JAA26174; Fri, 26 Jan 1996 09:02:37 -0500 (EST) Received: by ocserv.chemie.uni-hamburg.de (AIX 3.2/UCB 5.64/4.60) id AA25115; Fri, 26 Jan 1996 14:49:07 +0100 From: brock@chemie.uni-hamburg.de (Mathias Brock) Message-Id: <9601261349.AA25115@ocserv.chemie.uni-hamburg.de> Subject: orbital density viewers To: chemistry@ccl.net Date: Fri, 26 Jan 1996 14:49:06 +0100 (NFT) Cc: brock@chemie.uni-hamburg.de (Mathias Brock) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Status: RO Hallo netters, I investigated the document about MO visualizers and found a lack of electronic structure viewers. Most often just the molecular structures were visualized. The few suitable programs were used on specific hardware platforms thus PC's-based programs were scarce. In connection to MS-Windows-based text-processing I'm looking for a program generating electronic density graphics from G9x-output. It shall be great to have isosurfaces for planes through a molecules. Anybody, who has found or writen programs doing this, should be free to mail me about their experience. I'll summaries on the net. Mathias Brock From hey@mail2.nmri.nnmc.navy.mil Mon Jan 29 13:57:29 1996 Received: from mail2.nmri.nnmc.navy.mil for hey@mail2.nmri.nnmc.navy.mil by www.ccl.net (8.6.10/950822.1) id NAA27911; Mon, 29 Jan 1996 13:39:24 -0500 Date: Mon, 29 Jan 1996 13:39:24 -0500 Message-Id: <199601291839.NAA27911@www.ccl.net> Received: from transfusion.nmri.nnmc.navy.mil ([131.158.70.224]) by mail2.nmri.nnmc.navy.mil with SMTP; Mon, 29 Jan 1996 13:37:43 -0500 (EST) X-Sender: hey@mail2.nmri.nnmc.navy.mil (Unverified) X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Jeff Hey Subject: AMBER query reply summary Dear Fellow-CCL subscribers, Firstly thanks to all who replied to my queries. This email is a summary of the suggestions sent to me regarding the question of AMBER bending parameters for saccharides. I have not yet had time to view these references, but I will post them all regardless. The suggested references for AMBER bending parameters for saccharides are: Woods, et al., J. Phys. Chem., 1995, 99, 3832-3846. Glennon, et al., J. Comp. Chem., 1994, 15, 1019-1040. Imberty, et al., Glycobiology, 1991, 1, 631-642. (for Sybyl) Ha, et al., Carbohydrate Research, 1988, 180, 207. (Thanks to Dr J Brown) Yajun Zheng et al., J. Comput. Chem. 1994, 15,1019-1040. (Thanks to Yajun Zheng) Steve Homans, Biochem, 29, 9110-9118 (1990). (Thanks separately to Jeff Dyason and Alan Arnold [hello to some fellow Aussies!]) Also Kenny Lipkowitz (thanks!) wrote to tell me that Appendix I by Osawa and Lipkowitz in "Reviews in Computational Chemistry", vol. 6, VCH Publishers, 1995 is entitled "Published Force Field Parameters", and should contain the parameters that I need. In addition to all the above information, I was told that there is an AMBER web site, at http://www.amber.ucsf.edu/amber/amber.html. Thanks to Bill Ross and Soaring Bear for this information. I think that is all-apologies to those that I have accidentally left out of this summary! Jeff ******************************************************************* Dr Jeff Hey Transfusion and Cryopreservation Research Program NMRI, Building 29, Naval Medical Centre, Bethesda, Maryland, 20889-5607. Telephone: (301) 295 6378 FAX: (301) 295 6083 E-mail: hey@mail2.nmri.nnmc.navy.mil ******************************************************************* From mito@badoit.chem.nagoya-u.ac.jp Fri Jan 26 03:52:21 1996 Received: from badoit.chem.nagoya-u.ac.jp for mito@badoit.chem.nagoya-u.ac.jp by www.ccl.net (8.6.10/950822.1) id DAA11302; Fri, 26 Jan 1996 03:43:14 -0500 Received: (from mito@localhost) by badoit.chem.nagoya-u.ac.jp (8.6.11/8.6.9) id RAA13028; Fri, 26 Jan 1996 17:45:20 +0900 Date: Fri, 26 Jan 1996 17:45:20 +0900 From: Masakatsu ITO Message-Id: <199601260845.RAA13028@badoit.chem.nagoya-u.ac.jp> To: chemistry@www.ccl.net Subject: Any model Hamiltonian of polyene(C4H6,C6H8,C8H10)? Dear CCLers, I'm interested in the photoisomerization dynamics of polyenes. Does anyone know the literature concerning the model potential of those and parametrization? Any hints or comments concerning this subject are welcomed. I will post the summary of the responses if there would be any. Masakatsu Ito, PhD student Department of Structual Molecular Science The Graduate University for Advanced Studies Tel 81(Japan)-52-789-3656 Fax 81(Japan)-52-789-3551 E-mail mito@aqua.chem.nagoya-u.ac.jp Web http://www.chem.nagoya-u.ac.jp/~mito/mito.html From owner-chemistry@ccl.net Fri Jan 26 10:22:25 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id KAA14632; Fri, 26 Jan 1996 10:20:19 -0500 Received: from SANDCASTLE.COSC.BROCKU.CA for jmiller@SANDCASTLE.COSC.BROCKU.CA by bedrock.ccl.net (8.7.1/950822.1) id KAA27340; Fri, 26 Jan 1996 10:20:15 -0500 (EST) Received: from [139.57.81.109] by SANDCASTLE.COSC.BROCKU.CA via SMTP (950911.SGI.8.6.12.PATCH825/940406.SGI) for id KAA18185; Fri, 26 Jan 1996 10:20:02 -0500 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 26 Jan 1996 10:23:13 -0400 To: CHEMISTRY@ccl.net From: jmiller@SANDCASTLE.COSC.BROCKU.CA (Jack Martin Miller) Subject: Re:Semi-empirical programs for teaching Below is a summary of responses I received in answer to my request for advice on free or low cost semi-empirical programs for teaching purposes so that students might have copies for their own computers. Information is in the order recieved. My thanks, and that of my colleagues to all respondents. One of my coleagues has ended up using MOPAC, another GAMES, and several SPARTAN (currently on SGI, but the Mac version is awaited). 1.I don't know if this is what you are looking for, but we are about to release MacSpartan for the PowerMac platforms. Currently, you can acquire information from our WEB site at http://www.wavefun.com. MacSpartan is due to be released during the first quarter of 1996. MacSpartan includes: 1. A Graphical User Interface, much like Spartan for UNIX systems, that includes BUILDERS for: A. Organic Molecules B. Polypeptides C. Transition States 2. Calculations using the following methodologies: A. Molecular Mechanics (SYBYL) B. Semi-Empirical (AM1) C. Ab Initio Hartree-Fock (3-21G and 6-31G* basis sets) 3. Displays: A. Structure B. Molecular Orbitals, electron densities, electrostatic potentials C. Animation MacSpartan will run on all PowerMac platforms with 16MB of RAM, preferably with a 66MHZ processor or faster. All appropriate screens are supported, but the minimum for practical use is 13" and ideal is 16"/17" or greater. Obviously, the faster the machine, the better the performance--and your 8500 will more than do the job. And...the academic price for MacSpartan is only $299! If you have any further questions or are interested in acquiring MacSpartan, please get in touch with me at the address below. Thanks for your interest. Jim Parisi Marketing/Sales Coordinator 2. MNDO source code is available from the QCPE at Indiana University. Also, it is not semi-empirical, but I have a nice little version of an ordinary Huckel (that is, pi systems only; energies in units of beta) program, including parameters for heteroatoms, and an instruction manual. I'd be happy to make it available, free of course, on my ftp site. Professor Ray Fort, Jr. Voice: (207)-581-1180 Department of Chemistry FAX: (207)-581-1191 University of Maine E-mail: rcfort@maine.maine.edu Orono ME 04469 rfortjr@fort.umeche.maine.edu 3. I have two Macintosh HMO programs: 1) HMO written by Harry Haddon and John Farrell at Franklin and Marshall College in Lancaster, PA. It is quite old now: 1985 version. I don not know if it has been updated. A so-so program. 2) HMO written by Allan Wissner, Oncology and Immunology Section, Medical Research Division, American Cyanamide Co., Lederle Labs, Pearl River, NY 10965. This program would be nicely suited to Chemistry seniors. It displays the MOs graphically, which can be copied and included in text, etc. It also has an implementation of the "omega" technique. This one was *free* at the time!!! I searched the net for HMO (got many Health Management Orgs. hits) and Huckel + HMO and got no hits. Apparently these programs are not supported on the net. Hope this helps! GN Gary Newton Professor of Chemistry University of Georgia Chemistry Department Athens, GA 30602 USA Phone 706-542-1969 Fax 706-542-9454 email newton@sunchem.chem.uga.edu 4. Inquire about MOBY: there is an advert for MOBY 1.5 on p A27 of J Chem Ed, 1994 Feb (Springer Verlag, Electronic Media Dept, 175 Fifth Ave, New York, NY 10010, Tel (212)460-1653. Errol Lewars, Trent University ==== 5. Jack, MOPAC for DOS is very good. The only thing I'm not happy about is it doesn't have a graphical interface to create Input with. You have to literally type in the numbers describing the geometry in order to create an Input, whihc is very prone to error. I've never done this. Fortunately my advisor spent ca. $1000 buying CAChe package including MOPAC and its Editor. The latter is a chemistry-informed drawing program. I can use it to create a correct MOPAC Input for any platform including DOS. I have a feeling that somewhere on the Internet there's a program we can use in place of my CAChe Editor. Somebosy suggested SYBIL but the free version can only accept 10 (?) atoms which is too small for me. If you get a response about such a program, please let me know. Thank you. Yong y0h8797@acs.tamu.edu 6. Hi, I am not sure if this is what you are looking for but the price is right. My group produces the GAMESS ab initio package which includes several semi-emperical wavefunctions (AM1, PM3...). It runs on most workstations and on PowerMacs. If you are interested you can check out our WWW page at http://www.msg.ameslab.gov/ or send an email to Mike Schmidt at mike@si.fi.ameslab.gov to request a copy. There is no charge, but we do require that you sign a simple license agreement. Brett -- 7. I think Mopac95 is a good choice. It is easy to get the source code on the Internet. In addition, there are few freeware of drawing molecules and those data format could be converted by "babel"(also freeware). xxx name withheld on request. 8. Spartan is coming out with desktop computer versions which, although not cheap, probably cost about the same as many textbooks students are accustomed to paying for. I would appreciate receiving a summary of responses to this question. __________________________________________________________ Abby Parrill Chemistry Department Artificial Intelligence in Chemistry Laboratory The University of Arizona abby@mercury.aichem.arizona.edu __________________________________________________________ 9. Hello, Contact Serena Software Co in Bloomington, INDIANA They have made semi-empirical package MOPAC available for PC/Mac. Price very nominal. Ramesh 10. MacSpartan (PowerMac version) could do the job. It includes quantum mechanics (ab initio and semiempirical) and molecular mechanics methods. Its high-end graphics provides great visual teaching tools for organic chemistry. It prices at $299 (US & Canada academics). Along with it, Wavefunction also offers publications related to your purpose - teaching in organic chemistry: (1) Educational CD-ROM: "Visualization of chemical structures and reactions", (facusing on organic chemistry), by Tom Hehre, Lonnie Burke, Wayne Huang, Warren Hehre, 1995. (2) Self-guided Tutorial: "A MacSpartan Tutorial", Wavefunction, 1996. (3) Experiment book: "A Laboratory Book of Computational Organic Chemistry" by Warren Hehre, Wayne Huang & Alan Shusterman, 1996. For more information, check http://www.wavefun.com/MacSpartan.html --Wayne 11. and Ralph Puchta's summary of responses to his similar question. >Dear CCL-Users! > >1. Does anyone know free semiempirical calculation program, that are not > versions of ampac and mopac. >2. Which was the last free version of ampac? >3. Are there any free forcefield calculating programs? >4. On which ftp-server can I find these programs? > >Thank you very much for your help > >Ralph Puchta *************************************************************************** Here is my summary - and many thanks to all that wrote to me and helped. >1. Does anyone know free semiempirical calculation program, that are not > versions of ampac and mopac. There is a program called VAMP, that should be free up to VAMP 4.5. >2. Which was the last free version of ampac? All the MOPAC programs with single digit extensions, e.g. MOPAC 5, MOPAC 6, MOPAC 7, are public domain, and are `free'. Jimmy Stewart jstewart@fujitsu.com (Dr. James Stewart) >4. On which ftp-server can I find these programs? You can find free versions of MOPAC6 & MOPAC7 for DOS, LINUX and sources at www.ccl.net. Look in the webpage of CCL. I couldn't compile MOPAC7 for the SGI. Dr.Edgardo Garcia Cristol Chem & Biochem University of Colorado at Boulder ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++End A word to VAMP: I know it, as we use the newest version, that you have to buy, on our workstations in the university. If you can handle MOPAC5 to MOPAC7 you can handle VAMP also very good. AMPAC is also as suitable, but in my oppinion the available versions on ftp are to old, MOPAC is much newer. MOPAC is now developed also for buying, but if you look in chemical newspapers, there are still a lot of articels, that were calculated with MOPAC6. I personal run MOPAC6 on my PC by using DOS and by using LINUX. I have to point out the version compiled for LINUX is faster. The general handling is the same. The geometric input for the molecules and nearly all keywords are the same. So MY PERSONAL hint for your problem "no money - good results" is use MOPAC. A friend of mine used archie and gave me the following. here you can find MOPAC and related things. Host www.ccl.net (128.146.36.48) Last updated 03:47 5 Aug 1995 Location: /pub/chemistry/documents DIRECTORY drwxr-xr-x 512 bytes 00:00 22 May 1994 mopac_doc Location: /pub/chemistry/documents/mopac_doc FILE -rw-r--r-- 521604 bytes 23:00 6 Oct 1992 mopac6.doc FILE -rw-r--r-- 494856 bytes 00:00 16 Nov 1992 mopac6.ps Location: /pub/chemistry/software/DEC-ALPHA DIRECTORY drwxr-xr-x 512 bytes 00:00 1 Dec 1994 mopac6 Location: /pub/chemistry/software/MS-DOS/mopac_for_dos DIRECTORY drwxr-xr-x 512 bytes 10:51 17 Feb 1995 mopac6 Location: /pub/chemistry/software/OS-2 DIRECTORY drwxr-xr-x 512 bytes 00:00 1 Dec 1994 mopac6 Location: /pub/chemistry/software/LINUX DIRECTORY drwxr-xr-x 52 bytes 14:34 27 Jun 1995 mopac7 Location: /pub/chemistry/software/MS-DOS/mopac_for_dos DIRECTORY drwxr-xr-x 512 bytes 16:53 16 Mar 1995 mopac7 Location: /pub/chemistry/software/LINUX/mopac7/older_version_do_not_take FILE -rw-r--r-- 618 bytes 00:00 18 Aug 1994 mopac Host ftp.uni-koeln.de (134.95.100.202) Last updated 05:16 3 Aug 1995 Location: /usenet/comp.archives/bionet/chemistry DIRECTORY drwxrwxr-x 2048 bytes 22:00 22 Apr 1993 mpac Host www.ccl.net (128.146.36.48) Last updated 03:47 5 Aug 1995 Location: /pub/chemistry/software/LINUX/mopac7/older_version_do_not_take FILE -rw-r--r-- 811586 bytes 00:00 19 Aug 1994 mopac7.Z Location: /pub/chemistry/software/MS-DOS DIRECTORY drwxr-xr-x 512 bytes 10:51 17 Feb 1995 mopac_for_dos Location: /pub/chemistry/software/MS-DOS/mopac_for_dos/mopac6 FILE -rw-r--r-- 627791 bytes 00:00 22 Dec 1993 mopac.exe.Z FILE -rw-r---- 471300 bytes 00:00 22 Dec 1993 mopacdos.zip Location: /pub/chemistry/software/MS-DOS/mopac_for_dos/mopac7 FILE -rw-r--r-- 585910 bytes 16:45 16 Mar 1995 mopac7b.zip Location: /pub/chemistry/software/MS-DOS/mopac_for_dos/mopac7/old-version.95.02.17 FILE -rw-r--r-- 389585 bytes 11:03 17 Feb 1995 mopac7b.zip Location: /pub/chemistry/software/MS-DOS/mopac_for_dos/mopac7 FILE -rw-r--r-- 540413 bytes 16:46 16 Mar 1995 mopac7s.zip Location: /pubchemistry/software/MS-DOS/mopac_for_dos/mopac7/old-version.95.02.17 FILE -rw-r--r-- 359562 bytes 11:03 17 Feb 1995 mopac7s.zip Location: /pub/chemistry/software/MS-DOS/mopac_for_dos/mopac7/junk-do-not-look-here FILE -r-xr-xr-x 3541222 bytes 11:04 10 Mar 1995 mopac7.dos.big FILE -r-xr-xr-x 1725514 bytes 11:04 10 Mar 1995 mopac7.dos.sml Location: /pub/chemistry/software/OS-2/mopac6 FILE -rw-r--r-- 491975 bytes 00:00 1 Dec 1994 os2mopac.zip Location: /pub/chemistry/software/SOURCES/FORTRAN DIRECTORY drwxr-xr-x 512 bytes 00:00 22 May 1994 mopac6_sources DIRECTORY drwxr-xr-x 512 bytes 12:18 5 Jul 1995 mopac7_sources Location: /pub/chemistry/software/SOURCES/FORTRAN/mopac6_sources FILE -rw-r--r-- 1104875 bytes 00:00 23 Feb 1994 mopac6.tar.Z FILE -rw-r--r-- 857080 bytes 00:00 19 Mar 1994 mopac6.zip Location: /pub/chemistry/software/SOURCES/FORTRAN/mopac7_sources FILE -rw---r-- 331505 bytes 00:00 26 Jan 1995 mopac7-man-300.ps.Z FILE -rw-r--r-- 1487313 bytes 00:00 19 Aug 1994 mopac7-man-300.ps.Z.orig-does-not-work FILE -rw-r--r-- 378449 bytes 00:00 26 Jan 1995 mopac7-man-600.ps.Z For AMPAC try www.ccl.net: software/SOURCES/FORTRAN/mopac6_sources: total 2529 -rw-r--r-- 1 ccl 597133 Feb 23 1994 ampac21.tar.Z If you are looking for a visualistion tool for your outputs try CASCADE V2. This version is in the moment only for DOS/OS/WINDOWS available, but we hope that up to february we have CASCADE V3 running, it should run with DOS/OS/WINDWS and X. And the most interesting it is copyrighted as GNU - that meens free for all! For more infos about CASCADE, mail me, as I am a member of the CASCADE Development Team. As we do not have the chance to test CASCADE V3 on a X for MACs, I do not know if it will run on MAC too. Here is the text I mailed to the CCL some weeks ago. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++start Dear CCL users! We proudly announce our program CASCADE: Here the readme-file **************************************************************************** ***** C A S C A D E V 2 (DOS/Win/OS2 VERSION) ========================================================================== >> Cascade Aids Semi-empiric Calculators Access Displays Eventually :-) << ========================================================================== Cascade V2 is a shell which converts semi-empirical data (from programs like MOPAC, AMPAC and VAMP) into several 3d graphic formats. It thus enables the user to visualize the resulting molecule geometry. The supported display programs are: 3DV, Chemview, JMR, MOLWIN, MV, PC MODEL, PLUTON, POVRAY, RASWIN. -------------------------------------------------------------------------- Andreas Dosche (dosche@mi.uni-erlangen.de) Ralph Puchta (puchta@anorganik.chemie.uni-erlangen.de) Michael Reichenb"acher (reichenb@mi.uni-erlangen.de) -------------------------------------------------------------------------- Please use the program install.exe to uncompress cascade.zip, otherwise you have to set the environment variables CASCADE and AWKDIR manually. If you have used install.exe, you can use cascade.bat to start cascde. **************************************************************************** ***** You can get CASCADE via ftp: ftp://www.ccl.net/pub/chemistry/software/MS-DOS/cascade ftp://uni-stuttgart.de/pub/scivi/cascade You have to get 3 files: cascade2.rea -> the readme file (you have read in *) cascade2.zip -> the program install.exe -> this part installs CASCADE in the right way on your PC We hope that you will enjoy it. If you find any bugs or have any problems, think something should be changed, should be added or any thing else, feel free to contact us. We wish all CCl users a merry Christmas and a happy new year 1996. Andreas Dosche Ralph Puchta Michael Reichenb"acher ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++end I think you know most of the supported programs and you know, that they are free or not to expensive, too. If you want to combine the education in ab initio and semiempirical calculation, you can use GAMESS, that can do both, as they included parts of MOPAC. But I never tried it myself, for more infos try: Mike Schmidt via e-mail (mike@si.fi.ameslab.gov). As far as I know it runs on PC only via LINUX. About MAC I do not know anything. I fear GAMESS will not be supported in CASCADE V3, as I had not the time to get into GAMESS. To run Linux you need a PC 386 or higher, for running MOPAC5 you need also as 386 or hihger. I personal run my semie-empiric calculations at home on a 486 DX 2/66, and in order to calculate e.g. C60 it lasts a night. I hope this helped a little bit. Many greetings Ralph Puchta Puchta@anorganik.chemie.uni-erlangen.de Jack Martin Miller Professor of Chemistry Adjunct Professor of Computer Science Brock University, St. Catharines, Ontario, Canada, L2S 3A1. Phone (905) 688 5550, ext 3402 FAX (905) 682 9020 e-mail jmiller@sandcastle.cosc.brocku.ca http://chemiris.labs.brocku.ca/staff/miller/miller.html From smiguel@obelix.cica.es Mon Jan 29 06:01:52 1996 Received: from obelix.cica.es for smiguel@obelix.cica.es by www.ccl.net (8.6.10/950822.1) id GAA20205; Mon, 29 Jan 1996 06:01:34 -0500 Received: (from smiguel@localhost) by obelix.cica.es (8.7.1/8.7.1) id LAA19007 for chemistry-request@www.ccl.net; Mon, 29 Jan 1996 11:58:35 +0100 (GMT-1:00) Date: Mon, 29 Jan 1996 11:58:35 +0100 (GMT-1:00) From: Miguel Angel San Miguel Message-Id: <199601291058.LAA19007@obelix.cica.es> To: chemistry@www.ccl.net Hi netters, I am interested in getting slabs with different Miller indexes from unit cell. The slabs must be periodical in the other two directions. Do you know any book or reference about this problem? Is there any free software to generate these slabs?. I'll send a sumary with your answers Thanks in advance, Miguel Angel -------------------------------------------------------------- Miguel Angel San Miguel Barrera PhD Student Departamento de Quimica-Fisica Facultad de Quimica Universidad de Sevilla E-41012 Sevilla - SPAIN - Phone: 0034-5-455 71 77 FAX : 0034-5-455 71 74 e-mail: smiguel@obelix.cica.es From Jeffrey.Gosper@brunel.ac.uk Tue Jan 30 04:08:34 1996 Received: from monge.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.6.10/950822.1) id EAA09664; Tue, 30 Jan 1996 04:07:29 -0500 Received: from chem-pc-22.brunel.ac.uk by monge.brunel.ac.uk with SMTP (PP) id <02485-0@monge.brunel.ac.uk>; Tue, 30 Jan 1996 09:07:08 +0000 Date: Tue, 30 Jan 1996 09:07:04 GMT From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: WWW pages for Re_View with URL To: chemistry@www.ccl.net, ORGCHEM@EXTREME.CHEM.RPI.EDU, chem-education@mailbase.ac.uk Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear colleagues, sorry the last messages was missing the URL. Here it is again with the URL http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/re_view.htm I am pleased to announce that a WWW page has been setup to support my program Re_View as well as provide a range of information of relevance to molecular animations in general. If your not aware of Re_View, it's a Windows program that enables the visualization and analysis of dynamic reaction data such as conformational analysis, reaction pathways, vibrational modes, etc. I find it very useful both in research (particularly in examining MOPAC outputs) and in teaching undergraduates about such data. The site provides general information about the program, a free demonstration version of Re_View, a number of example molecular animations/simulations (both a coordinates and as movies), pointers to other relevant pages, and also a program that aids in the analysis of MOPAC IRC calculations. Please take a look at the site and if you feel that you have information and/or a WWW page that should be included please let me know. /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://http1.brunel.ac.uk:8080/~castjjg \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From gerwens@mbox.theochem.uni-hannover.de Tue Jan 30 09:38:39 1996 Received: from mgate.uni-hannover.de for gerwens@mbox.theochem.uni-hannover.de by www.ccl.net (8.6.10/950822.1) id JAA13610; Tue, 30 Jan 1996 09:37:56 -0500 From: Received: from sun1.rrzn-user.uni-hannover.de (actually sun1.rrzn.uni-hannover.de) by mgate.uni-hannover.de with SMTP (PP); Tue, 30 Jan 1996 15:36:13 +0100 Received: by sun1.rrzn-user.uni-hannover.de (5.0/SMI-SVR4) id AA01794; Tue, 30 Jan 1996 15:36:11 +0100 Message-Id: <9601301436.AA01794@sun1.rrzn-user.uni-hannover.de> Subject: Electrost.Pot.Biomol;Graphic Software? To: chemistry@www.ccl.net (CCL CCL) Date: Tue, 30 Jan 1996 15:36:08 +0100 (MET) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 2319 Dear CCLers, I'm working on a model to calculate the electrostatic potentials of Biomolecules, e.g. Proteins. This model is based on the ADM-model (J.Chem.Phys. 99,1224 (1993)), which gives you a good approximation of the electrostatic potential of small molecules. For this model you need atomic charges and dipole moments (CAMMs), which have to be calculated from a wavefunction using some population analysis. In the original ansatz ab initio 6-31G* SCF wavefunctions were used to calculate the CAMMs with the Mulliken population analysis. In my work I'm trying to model these CAMMs (atomic charges and dipoles) and to use these CAMMs to calculate the electrostatic potentials of large proteins. In the model, to calculate the CAMMs, intramolecular polarization is included. Besides the electrostatic potential the ADM-model also provides an approximation of the electronic density. Therefore the isodensity surfaces of such large molecules are easy to access. The isodensity surfaces are a valuable tool to interpret the shape of a system. My aim is to represent the electrostatic potential of proteins on their isodensity surfaces. Currently the isodensity surfaces are calculated with the 'Marching Cube' Algorithm (J.Comp.Chem. 14,246 (1993)). Now the questions: a) The graphical tools I currently use to draw the electrostatic potential on the isodensity surfaces are inadequate to use for such a large system as a protein. I'm looking for a graphical device, which is able to handle this problem. It should be able to draw the surface triangles created by the Marching Cube algorithm at a rate of 10,000 per second. b) I'm looking for a cooperation with somebody, who is interested in the application of my model. As input data for the model only cartesian coordinates of all atoms (including hydrogen) of a protein are required. As output data you get atomic charges and atomic dipole moments. With the ADM-model electrostatic potentials on isodensity surfaces can be calculated. Applications which directly interpret the electrostatic potential would be nice. Currently metal atoms are not feasible. Heiko Gerwens Institut fuer Theoretische Chemie Universitaet Hannover Am Kleinen Felde 30 D-30167 Hannover Germany email: gerwens@mbox.uni.hannover.de From joubert@ext.jussieu.fr Tue Jan 30 10:08:39 1996 Received: from shiva.jussieu.fr for joubert@ext.jussieu.fr by www.ccl.net (8.6.10/950822.1) id KAA14601; Tue, 30 Jan 1996 10:04:47 -0500 Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.6.10/jtpda-5.1) with ESMTP id QAA18915 for ; Tue, 30 Jan 1996 16:03:15 +0100 Received: from [134.157.11.17] by idf.ext.jussieu.fr (8.6.10/jtpda-4.0) with SMTP; Tue, 30 Jan 1996 16:03:04 +0100 X-Sender: joubert@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 30 Jan 1996 16:07:49 +0100 To: chemistry@www.ccl.net From: joubert@ext.jussieu.fr (JOUBERT laurent) Subject: Semi-empirical with lanthanides Hi all, Does anybody know a semi-empirical program working with lanthanides and actinides ? Thanks in advance for your answers. Laurent JOUBERT ------------------------------------------------------------------ JOUBERT Laurent Ecole Nationale Superieure de Chimie de PARIS Laboratoire de Modelisation appliquee a la Chimie et aux Procedes 11, rue Pierre et Marie Curie 75005 PARIS - FRANCE E-Mail : joubert@ext.jussieu.fr Tel : 44-27-66-94 Website : http://www.enscp.jussieu.fr ------------------------------------------------------------------ From ysandler@post.smu.edu Tue Jan 30 10:23:39 1996 Received: from post.cis.smu.edu for ysandler@post.smu.edu by www.ccl.net (8.6.10/950822.1) id KAA14828; Tue, 30 Jan 1996 10:16:27 -0500 Received: by post.cis.smu.edu (/\==/\ Smail3.1.28.1 #28.1) id ; Tue, 30 Jan 96 09:16 CST Date: Tue, 30 Jan 1996 09:16:22 -0600 (CST) From: Yakov Sandler Subject: propellanes To: chemistry@www.ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, everyone! I am intersted in studying bonding in propellanes. It was reported ( Kenneth B. Wiberg et al. J. Am. Chem. Soc. 1982, 104, 5240-5242), that localized orbital calculations suggest that the central bond in [1.1.1]propellane has a bond order close to zero. I used spartan to calculate the natural bond order in this molecule. My ab initio (HF/6-31G*) calculation showed that the C1 and C2 of the central bond have different electron density distribution, and (!) each one of them has a different BOs in bonds with atoms 3, 4, and 5, even though the starting geometry is perfect D3h! My question is if anyone has dealt with this problem and can give me a hint of what is going on. Also, are there any references to recent developments in this area. Thanks in advance Yakov I. Sandler Southern Methodist University ysandler@post.cis.smu.edu From owner-chemistry@ccl.net Tue Jan 30 10:38:40 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id KAA15046; Tue, 30 Jan 1996 10:26:10 -0500 Received: from chem.duke.edu for taisung@chem.duke.edu by bedrock.ccl.net (8.7.1/950822.1) id KAA13020; Tue, 30 Jan 1996 10:26:06 -0500 (EST) Received: from teller.chem.duke.edu (teller.chem.duke.edu [152.3.169.113]) by chem.duke.edu (8.7.1/Duke-1.1) with ESMTP id KAA25685; Tue, 30 Jan 1996 10:26:04 -0500 (EST) Received: (taisung@localhost) by teller.chem.duke.edu (8.7.1/Duke-1.1) id KAA21509; Tue, 30 Jan 1996 10:26:04 -0500 (EST) Date: Tue, 30 Jan 1996 10:26:03 -0500 (EST) From: Taisung Lee To: chemistry@ccl.net Subject: Summary: Good Fortran Compiler for computational science on PC Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Several weeks ago I posted a question about Fortran compiler and I got much nice and useful information. Thanks to all repliers. Taisung Lee Here is the summary: From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Lahey is widely regarded as the best Fortran compiler for Pentium platforms. They also have a Fortran 90. Few people find that actual performance on real-world codes parallels any "standard" benchmarks, such as specfp92. We'll all be interested in hearing comparative benchmarks for your quantum code on Pentium and IBM RISC. -P. From nash@chem.wisc.edu Thu Jan 4 22:18:19 1996 I am an end-user of computational software for chemistry, and I have been glad to see useful computational packages showing up on desktop computers. When looking for a "PC" platform to develop for, don't forget the one that uses same RISC technology that those RS6000s do, i.e. the PowerPC. The FORTRAN-coded quantum package GAMESS has been successfully ported to PowerMac, and the authors state: >Most operating systems on the IBM PC (and its clones) are too small to run >GAMESS. Typically >GAMESS compiles to over 8 MBytes of object code alone, making it difficult >to work with most >PC operating systems. There are also too many different compilers and >floating point coprocessor >options for us to attempt to maintain a PC version. Therefore we do not >have any version of >GAMESS for DOS, Windows, NT, or OS/2. NT and OS/2 would be capable of running >GAMESS but you are on your own if you wish to try it. This "big, real" computational program was compiled using Language Systems FORTRAN for PowerMac. Overall run times are about 3 times an IBM RS6000 model 350 on a PM7100/66. The cost-to-computational-power ratio is rather nice! Another quantum mechanical program on this platform is the newly-released MacSPARTAN. There's more than FORTRAN code to that, of course, but it illustrates the utility of the system as a viable computational workstation. I have no affiliation with Apple other than being a satisfied PowerMac customer. If you have significant investment in CISC-based systems, or strong operating system biases, this may not be an option, but FORTRAN-based chemistry code on the PowerMac is certainly possible and runs quite impressively. Relevant URL: http://www.msg.ameslab.gov/GAMESS/GAMESS.html -john nash, UW-Madison From landman@motown.detroit.sgi.com Thu Jan 4 22:57:40 1996 On the QMD code I use, this the the approx performance table: (single cpu times only) cpu OS time (in seconds) per time step --------------------------------------------------------------- 486/DX33 OS/2 Warp 3000 (memory starved at 8 meg) R3000/40MHz IRIX 5.3 900 SuperSparc/33MhzSolaris 700 Pentium/133MHz OS/2 Warp 290 (64 Meg ram) R4400/150MHz IRIX 5.3 126 (Indy w 96 meg ram) RS6000/590 AIX 120 Cray J90 Unicos 87 Alpha/266 OSF1 82 R8000/75MHz IRIX 6.1 55 (2 meg cache, 384 meg ram) R8000/90MHz IRIX 6.1 47 (4 meg cache, 2 gig ram) (no data on R10k ... yet :-) ) 64 atom supercell, same configuration and input file on all machines. THe fortran compiler on the PC was the Watcom 9.01e, and the combination of gcc/emx and f2c (which did quite well). The Pentium unit is my advisors home PC that we are using for additional cycles for the rest of the group. THe R8k times are low as a result of my optimizing the time consuming portions of the code to make use of fused multiply add instructions and working very hard to get a good instruction scheduling out of the compiler. I used a 64 atom supercell as my standard test as that is what I tend to work with. When I go to larger supercells, all but the largest memory machines quit. At 512 atoms, even the powerchallenge is spending more time swapping (with 4 GB ram installed) than computing. My thoughts are that the Pentium133 and higher with sufficient ram and a FAST disk (the current crop of ATA4 are not as fast as SCSI II) ought to be a good cheap entry level workstation for development and testing work. I prefer an Indy, but I think I am biased (see the .sig). For the production medium and big runs, you really do need to look at the heavy metal (the superworkstations). Run a stable OS on the box such as Linix or OS/2 Warp Connect and the machine will be very useful. Joe From: "Walter E. Reiher III" Related issues have been raised here before, so I'm responding to the list: I've spent an inordinate amount of time over the past year and a half or so fiddling around with PC FORTRAN compilers, and the bottom line, IHMO, is that you'd better not count on them being like what you're accustomed to under UNIX. In general, PCs seem like a false economy to me. There are two issues here: the compiler and the operating system. You don't mention which OS you're using, but MS FPS only runs under NT or Win95. If you're running Win95, or DOS/Win, that's the first thing to get rid of. Windows NT is a reasonable OS; many say OS/2 is also. There are also UNIXes available for Intel CPUs. Just don't waste your time with a 16 bit OS like DOS or a hybrid 16/32 system like 95. Many 'big program' problems are related to trying to run in 16 bits or tricking a 16 bit OS into looking like a 32 bit one. How long has it been since we're tried doing this with UNIX? Years! Who needs to go back to _that_? On compilers, I've worked with three--Watcom, MS FORTRAN PowerStation 32 (predecessor to 4.0), and Absoft--and all of them have some problems for my applications, which involve mixed FORTRAN and C programming and interoperability with a MS Visual C++ graphics DLL. Watcom had loads of incompatibility problems and really poor tech support, but produces fast code when you can make it work. MS FPS also produces fast code and has a nice development environment, but has surprisingly poor interoperability with C. I'm continuing to use Absoft, who has excellent tech support and C interoperability but produces slow code on a Pentium and has some other quirks. Other compiler vendors I have not tried include Salford (a British company; expensive compiler but it must be a 'real' one since all of Chem-X builds under it), Microway NDP, and Lahey. BTW, I've only used these as FORTRAN 77's, not 90's. If you don't need to worry about working with C and calling DLLs, life will probably be easier for you. It seems to me that FORTRAN really isn't taken seriously by the compiler vendors--the emphasis is on C/C++. I was disappointed to learn this week that the FORTRAN on my 'reference' platform, the SGI, also isn't what it used to be. Some switches that I found valuable for finding bugs in old code on my old IRIX 5.2 system are missing on my new IRIX 6.1 system (e.g., -trapuv and -u). See the "SciTech Software for Science" catalog for a comprehensive list of FORTRAN compilers and other technical software tools. 800-622-3345, http://www.scitechint.com/scitech/. I'm not affiliated with them. Hope this helps...good luck. I'd be interested in hearing the experiences of others. Wally ======================================================================== Walter E. Reiher III, Ph.D. Wally@CompChem.com CompChem Innovations P.O. Box 61056 voice 408-720-0240 Sunnyvale, CA 94088 fax 408-720-0378 From: Craig Taverner We use PC's as computational tools extensively in crystallography, but we run them all (the computational ones that is) under LINUX for which f77 is freely available (g77 and f2c), and we also have the NAG f90 compiler, which so far seems to compile fine with true fortran 90 programs, but has proved to be somewhat tricky with fortran 77 programs. Unfortunately I have not used it nearly enough to give you any performance spec.'s or say whether it can cope with very large programs, but I should certainly expect it to be able to. So far our experience with using Linux instead of Dos/windows has definitely demonstrated it to be more appropriate for computational work. Contact NAG at: NAG Ltd NAG Inc tel +44 (0)1865 311744 +1 708 971 2345 fax +44 (0)1865 311755 +1 708 971 2346 post NAG Response Centre NAG Response Center NAG Ltd NAG Inc Wilkinson House 1400 Opus Place Jordan Hill Road Suite 200 OXFORD Downers Grove United Kingdom IL 60515-5702 OX2 8DR USA email infodesk@nag.co.uk infodesk@nag.com www http://www.nag.co.uk gopher NAME=NAG Gopher Server, Type=1, Port=70, Path=1/, Host=www.nag.co.uk This is straight from their magazine, verbatum. I hope it's not overboard. Cheers, Craig "If God had meant us to be naked, we would have been born that way." Craig Taverner Structural Chemistry, University of the Witwatersrand, South Africa From: Guo Jian-xin Hi, Your question about the compiler maybe get: The NDP fortran compiler is good as the microft fortran complier. It is a better choice. regards, J.X. Guo From: frits@chemde4.leidenuniv.nl (Frits Daalmans) hello, I think that NAG (Numerical Algorithms Group) sells a Fortran 90 compiler for Linux. Lemmesee... no, sorry, I don't have more information. Greetings, Frits Frits Daalmans OIO Conformational Analysis Gorlaeus Laboratoria Leiden, The Netherlands E-mail: frits@chemde4.leidenuniv.nl Tel: [+31] (0)71-5274505 From: jochen@sunserver1.rz.uni-duesseldorf.de Yeah, it is FORTRAN 90, maybe it's NAG. If it is not YAG, I will tell you after I asked my friend. Jochen From: rbw@msc.edu (Richard Walsh) Taisung, You should try Absoft at 810-853-0050 (www.absoft.com). They have F77 and F90 for PC. Their F90 is compatible with the F90 on Cray platforms so you codes should compile error free on either machine. The same F90 is available for SUNs and I will be made available for other workstations in the future. Richard Walsh Minnesota Supercomputer Center, Inc. P.S. They also have compilers for Macs I think. From: case@scripps.edu (David Case) I'd be interested to know what sorts of errors you encountered, and on which OS. Do the errors show up in F77 code, or in the F90-specific parts? I have used this compiler on a P6/NT machine with good success on very large F77 molecular mechanics programs. ..thx...dac ================================================================== David A. Case | internet: case@scripps.edu Dept. of Molecular Biology, MB1 | bitnet: case%scripps.edu@sdsc The Scripps Research Institute | fax: 619-554-3789 10666 N. Torrey Pines Rd. | phone: 619-554-9768 La Jolla CA 92037 USA | WWW: http://scripps.edu/case ================================================================== From: zauhar@xhost5.tripos.com (Randy Zauhar) To: Taisung Lee Subject: Re: CCL:Good Fortran Compiler for computational science on PC? -------------------- Taisung, There is a company called Lahey (in Nevada, I believe) that specializes in FORTRAN compilers for PCs. I investigated their products a few years ago and was favorably impressed with what they offered, although I did not end up buying anything from them. They use to regularly have ads in BYTE magazine. If you cannot find their address, I think I still have some of their literature laying around. Randy All opinions expressed here are mine, not my employer's ///////////////////////////////////////////////////////////////////////// \\ Randy J. Zauhar, PhD | E-mail: zauhar@tripos.com // \\ Tripos, Inc. | : zauhar@crl.com // \\ 1699 S. Hanley Rd., Suite 303 | Phone: (314) 647-1099 Ext. 3382 // \\ St. Louis, MO 63144 | // ///////////////////////////////////////////////////////////////////////// ** ** ** "If you have conceptions of things that you can have no conception ** ** of, then the conception and the thing appear to co-incide." ** ** --- C.G. Jung ** ************************************************************************* From Patrick.Bultinck@rug.ac.be Tue Jan 30 11:08:40 1996 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.10/950822.1) id KAA15673; Tue, 30 Jan 1996 10:56:23 -0500 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA26744 (5.67b/IDA-1.5 for ); Tue, 30 Jan 1996 16:56:07 +0100 Received: from hartree1.rug.ac.be by allserv.rug.ac.be (5.x/SMI-SVR4) id AA29185; Tue, 30 Jan 1996 16:55:58 +0100 Date: Tue, 30 Jan 1996 16:53:34 +0100 (NFT) From: Patrick Bultinck To: CCL Subject: MMx studies of chelates Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, Can anybody point me to a good (meaning of good is explained later) reference to articles where studies of chelate complexes formed between ligands such ethylenediamine (or the glycol) and 1,3-propanediamine (or the glycol) and main group ions. By 'good' I mean an article from which I can also learn something on the method used (and NOT only the program used). E.g. what charge distributions were used, maybe atom types etc. Is it 'normal' that this very important information is usually neglected ? By simply taking another force field and parameters it is sometimes possible to conclude the entirely opposite ! Thanks, Patrick Bultinck Univ. of Ghent, Belgium From patnaiss@Picard.ml.wpafb.af.mil Tue Jan 30 11:38:40 1996 Received: from riker.ml.wpafb.af.mil for patnaiss@Picard.ml.wpafb.af.mil by www.ccl.net (8.6.10/950822.1) id LAA16315; Tue, 30 Jan 1996 11:26:16 -0500 Received: from picard.ml.wpafb.af.mil by riker.ml.wpafb.af.mil (5.65/Ultrix3.0-C) id AA15543; Tue, 30 Jan 1996 11:25:20 -0500 Received: by Picard.ml.wpafb.af.mil (4.1/version) id AA10051; Tue, 30 Jan 96 11:25:19 EST Date: Tue, 30 Jan 96 11:25:19 EST From: patnaiss@Picard.ml.wpafb.af.mil (Soumya S. Patnaik MLPJ UTC) Message-Id: <9601301625.AA10051@Picard.ml.wpafb.af.mil> To: chemistry@www.ccl.net Subject: looking for a rigid body minimization prog Dear Colleagues, I am looking for a program that would do minimization of the energy of association of two or more molecules while considering each molecule rigid. Does anyone have access to such a program? Thanks in advance Soumya Patnaik ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Dr Soumya S. Patnaik email: patnaiss@picard.ml.wpafb.af.mil + + Materials Laboratory, Wright Patterson AFB + + usmail: WL/MLPJ, Bldg 651, 3005 P St, Ste 1, WPAFB, OH 45433-7702 + + Telephone: (513) 255-6671 ext.3116 FAX: (513) 255-1128 + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-chemistry@ccl.net Tue Jan 30 12:23:41 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id MAA17672; Tue, 30 Jan 1996 12:08:53 -0500 Received: from astro.ocis.temple.edu for xiaopeng@astro.ocis.temple.edu by bedrock.ccl.net (8.7.1/950822.1) id MAA15968; Tue, 30 Jan 1996 12:08:49 -0500 (EST) Received: (from xiaopeng@localhost) by astro.ocis.temple.edu (8.7.1/8.7.1) id MAA12100; Tue, 30 Jan 1996 12:08:26 -0500 (EST) Date: Tue, 30 Jan 1996 12:08:24 -0500 (EST) From: Peking To: Mathias Brock cc: chemistry@ccl.net, Mathias Brock Subject: Re: CCL:orbital density viewers In-Reply-To: <9601261349.AA25115@ocserv.chemie.uni-hamburg.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Spartan can do this xiaopeng ======================================================= Chemistry Graduate student 215-2047149(office) 215-5357188(home) xiaopeng@astro.ocis.temple.edu ====================================================== On Fri, 26 Jan 1996, Mathias Brock wrote: > Hallo netters, > > I investigated the document about MO visualizers and found a lack > of electronic structure viewers. Most often just the molecular > structures were visualized. > The few suitable programs were used on specific hardware platforms > thus PC's-based programs were scarce. > In connection to MS-Windows-based text-processing I'm looking > for a program generating electronic density graphics from G9x-output. > It shall be great to have isosurfaces for planes through a molecules. > Anybody, who has found or writen programs doing this, should be free to mail > me about their experience. I'll summaries on the net. > > Mathias Brock > > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- > From vuckovic@hyper.com Tue Jan 30 12:38:41 1996 Received: from www.hyper.com for vuckovic@hyper.com by www.ccl.net (8.6.10/950822.1) id MAA17993; Tue, 30 Jan 1996 12:26:19 -0500 Received: (from vuckovic@localhost) by www.hyper.com (8.6.12/8.6.12) id MAA08975 for chemistry@www.ccl.net; Tue, 30 Jan 1996 12:34:17 -0500 From: Dragan Vuckovic Message-Id: <199601301734.MAA08975@www.hyper.com> Subject: HyperChem User Group Meeting - 1996 To: chemistry@www.ccl.net Date: Tue, 30 Jan 1996 12:34:16 -0500 (EST) X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 5621 Hypercube, Inc. presents the First World HyperChem User Group Meeting September 8-11, 1996 Clevelands House, Minett, Muskoka Ontario, Canada First Announcement HyperChem is like any other powerful tool: the more you know about it, the more you get from working with it. For those who wish to learn more about working with HyperChem, the range of problems you can now tackle on a PC, and for those who wish to show other people how HyperChem can be used successfully in various fields of chemistry, Hypercube, Inc. (the developers of HyperChem) offer The First World HyperChem User Group Meeting. Objectives of the Meeting There are many of you who are doing a remarkable job with HyperChem in the research and teaching fields. Additionally, there are certainly even more uses that we are not aware of, as to how you are using HyperChem. With this in mind, we would like to bring all of you together so that we can share ideas and information. Experienced HyperChem users will be invited to provide introductory talks, and we, at Hypercube, will be there to present our views of how HyperChem can be used and our vision of future developments of HyperChem. We would like to hear your suggestions, since HyperChem is made for you, the end user. A small computer lab will be available, so that after the official hours of the Meeting, we can exchange ideas, demonstrate and learn the new uses and applications of HyperChem; or you can simply enjoy the beach, pools, tennis courts, or other facilities of this beautiful resort in the middle of Muskoka county and gorgeous Muskoka lake. Outline of the Meeting The Meeting will be divided in three sections depending on particular HyperChem (or other Hypercube products) uses in: (A) Research (B) Teaching (C) Association with other programs The first section (A), HyperChem in Research, will cover all the fields in chemistry and biochemistry where HyperChem can be used. The second section (B), HyperChem in Teaching, will cover all the teaching levels of chemistry where HyperChem is used. The third section (C), HyperChem in Association with other Programs, will cover all the possible uses of HyperChem in conjuction with other programs in the Windows environment (automation using scripts or Excel Macros, etc.) as well as the use of HyperChem in association with other molecular modeling or quantum chemistry programs. Costs and Venue In order to organize this Meeting and to bring experts talk about HyperChem, a small Registration fee of $100.00 US for academic, and $150.00 US for commercial users will apply. The Meeting will be held at Clevelands House, a beautiful resort on the Muskoka Lake just about 200 km north of Toronto. The resort has excellent conference facilities, as well as many recreational facilities, including four swimming pools, beach on the lake, tennis courts, water sports, facilities for children, etc. Accommodation The accommodation for all the participants of the Meeting will be at Clevelands House (Approximate prices including all the meals, taxes, and recreational facilities: Single: $195.00 CAN; Double: $145.00 CAN). Participants will be expected to make their own reservation directly with Clevelands House. Detailed instructions will follow in the Second Announcement on receipt of the attached form. Transportation Participants will be expected to make their own travel arrangements to Toronto International Airport. Shuttle Bus service will be available from the Airport to Clevelands House on both September 7th and 8th, as well as for the return to the Airport on September 11th and 12th. The Second Announcement will give complete details about the shuttle bus service, as well as the directions on how to reach Clevelands House if you are traveling by car. Preliminary Registration To tentatively register for the Meeting and to receive the Second Announcement, please complete the enclosed form and return as soon as possible (before April 1) to: Dr. Dragan Lj. Vuckovic Hypercube, Inc. Unit 7, 419 Phillip Street Waterloo, Ont. Canada N2L 3X2 e-mail: vuckovic@hyper.com Tel. (519) 725-4040 Fax: (519) 725-5193 The Second Announcement will be mailed in April Preliminary Registration Form The First World HyperChem User Group Meeting Clevelands House, Muskoka, ON, Canada September 8-11, 1996 Please send me the Second Announcement. NAME __________________________________________________ ORGANIZATION __________________________________________________ POSITION __________________________________________________ ADDRESS FOR CORRESPONDENCE __________________________________________________ __________________________________________________ ___________________________________________________ TEL. NO. __________________FAX NO._________________ I am interested in attending the Meeting ___, or attending the Meeting and presenting a paper ___, in section A, B or C (circle the appropriate section). SIGNATURE DATE _____________________________________________________ ___________________________________________________________________ Dr. Dragan Lj. Vuckovic phone: (519) 725-4040 International Marketing Manager fax: (519) 725-5193 Hypercube, Inc. e-mail: vuckovic@hyper.com 419 Phillip Street URL: http://www.hyper.com Waterloo, Ontario Canada, N2L 3X2 From hinsenk@ERE.UMontreal.CA Tue Jan 30 14:53:43 1996 Received: from harfang.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.10/950822.1) id OAA21831; Tue, 30 Jan 1996 14:49:36 -0500 Received: from eole.ERE.UMontreal.CA (eole.ERE.UMontreal.CA [132.204.10.20]) by harfang.CC.UMontreal.CA with ESMTP id OAA08664 (8.6.11/IDA-1.6 for ); Tue, 30 Jan 1996 14:48:35 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (950221.405.SGI.8.6.10/5.17) id OAA07881; Tue, 30 Jan 1996 14:48:34 -0500 Received: by cyclone.ERE.UMontreal.CA (950221.405.SGI.8.6.10/5.17) id OAA25966; Tue, 30 Jan 1996 14:48:33 -0500 Date: Tue, 30 Jan 1996 14:48:33 -0500 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <199601301948.OAA25966@cyclone.ERE.UMontreal.CA> To: chemistry@www.ccl.net Subject: Python code for computational chemistry I have made some Python code for computational chemistry available at the CCL archive. It can be found via the URLs ftp://www.ccl.net:/pub/chemistry/software/SOURCES/PYTHON/HINSEN gopher://www.ccl.net:73/11/software/SOURCES/PYTHON/HINSEN For those who don't know Python, it's a high-level, object-oriented, interpreted general-purpose programming language. There is a free and reliable implementation that is being improved constantly by a growing community of users. There is already an impressive range of extension modules taking care of applications as diverse as Web browsers, databases, and numerical calculations. For more information point your Web browser at http://www.python.org. Here's a short description of the modules at the CCL archive: PDB.py High-level I/O with PDB files. Allows you to deal with PDB files as if they were lists of residues and atoms. Example: for residue in PDBConfiguration('protein.pdb'): for atom in residue: print atom.name, atom.position Derivatives.py Automatic derivatives. Calculates analytical derivatives numerically, given only the original function. Example: x = DerivVar(1.1,0) y = DerivVar(0.44, 1) f = exp(x**2+y**2) print f prints: (4.06982499598, [8.95361499116, 3.58144599646]) Potential.py Automatic gradient calculation for potential functions (or any function). Example: def harmonic(k, r1, r2): dr = r1-r2 return k*dr*dr harmonic_g = PotentialWithGradients(harmonic) energy, gradients = harmonic_g(100., Vector(0,3,1), Vector(1,2,0) print energy, gradients prints: 300.0 [Vector(-200.0,200.0,200.0), Vector(200.0,-200.0,-200.0)] Vector.py 3d-vectors, used by the three other modules. umath.py Simplified substitute for the module "umath" from the numerics package. Use it only if you don't have the numerics package. This module is used by all the other modules in this directory. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. Centre-Ville | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From xiaopeng@astro.ocis.temple.edu Tue Jan 30 15:53:44 1996 Received: from astro.ocis.temple.edu for xiaopeng@astro.ocis.temple.edu by www.ccl.net (8.6.10/950822.1) id PAA23059; Tue, 30 Jan 1996 15:39:54 -0500 Received: (from xiaopeng@localhost) by astro.ocis.temple.edu (8.7.1/8.7.1) id PAA06938; Tue, 30 Jan 1996 15:39:13 -0500 (EST) Date: Tue, 30 Jan 1996 15:39:12 -0500 (EST) From: Peking To: "Soumya S. Patnaik MLPJ UTC" cc: chemistry@www.ccl.net Subject: Re: CCL:looking for a rigid body minimization prog In-Reply-To: <9601301625.AA10051@Picard.ml.wpafb.af.mil> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 30 Jan 1996, Soumya S. Patnaik MLPJ UTC wrote: > > Dear Colleagues, > > I am looking for a program that would do > minimization of the energy of association of two or > more molecules while considering each molecule rigid. > > Does anyone have access to such a program? Thanks in advance I think that you can construct a z-matrix format of 2 molecule separately and then put them together, specify al the parameters in the molecule as constraints. so this just leaves 3 other parameters between 2 molecule not constraint(they are distance, angle, and diherdral angle betwwen the first atom of the 2nd molecule and another atom you choose from the 1st molecule) . Then you just submit the job in G94 This does work, but a little lousy to specify the constraints xiaopeng ----------------------------------------------------------------- Chemistry Graduate Student 215-5357188(home) 215-2047149(office) xiaopeng@astro.ocis.temple.edu ----------------------------------------------------------------- > > Soumya Patnaik > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > + Dr Soumya S. Patnaik email: patnaiss@picard.ml.wpafb.af.mil + > + Materials Laboratory, Wright Patterson AFB + > + usmail: WL/MLPJ, Bldg 651, 3005 P St, Ste 1, WPAFB, OH 45433-7702 + > + Telephone: (513) 255-6671 ext.3116 FAX: (513) 255-1128 + > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: patnaiss@Picard.ml.wpafb.af.mil > -- Original Sender From: Address: patnaiss@Picard.ml.wpafb.af.mil > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html >