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 chemistry-request@www.ccl.net Fri Jan 26 04:07:20 1996 Received: from harfang.CC.UMontreal.CA for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id DAA11447; Fri, 26 Jan 1996 03:56:05 -0500 Received: from meds1.MEDCN.UMontreal.CA (meds1.MEDCN.UMontreal.CA [132.204.11.103]) by harfang.CC.UMontreal.CA with ESMTP id DAA18450 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 03:55:15 -0500 Received: from harfang.CC.UMontreal.CA by meds1.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id IAA00578; Fri, 26 Jan 1996 08:56:31 GMT Received: from www.ccl.net (www.ccl.net [128.146.36.5]) by harfang.CC.UMontreal.CA with ESMTP id DAA18447 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 03:55:13 -0500 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id DAA11308; Fri, 26 Jan 1996 03:43:30 -0500 Received: from oceane.cict.fr for monceau@oceane.cict.fr by www.ccl.net (8.6.10/950822.1) id DAA11004; Fri, 26 Jan 1996 03:31:48 -0500 Received: from [] ([193.48.178.48]) by oceane.cict.fr (8.6.9/8.6.9) with SMTP id JAA04258 for ; Fri, 26 Jan 1996 09:30:54 +0100 Message-Id: <199601260830.JAA04258@oceane.cict.fr> X-Original-Sender: Sender: Computational Chemistry List From: "Daniel Monceau" To: CHEMISTRY@www.ccl.net Date: Fri, 26 Jan 1996 09:32:22 +1 Subject: CCL:post doc Reply-To: Daniel.Monceau@cict.fr Priority: normal X-mailer: Pegasus Mail/Windows (v1.22) Errors-To: ccl@www.ccl.net Precedence: bulk X-Caution: User has inserted an Explicit Reply-To ************** * Postdoctoral Position * ************** EC project: Human Capital and Mobility on High Temperature Corrosion Testing Location : Toulouse - France Salary : about 12000 FF. after charges and social security. This position is available now and for a duration of 12 or 16 months Contact : Daniel Monceau ENSCT URA 445 CNRS 118 route de Narbonne 31077 TOULOUSE FRANCE tel.: (33) 61-17-56-61 fax: (33) 61-17-56-00 e-mail: MONCEAU@CICT.FR Candidate: The candidate must have a European community nationality (but not French). He/she should know about one or several of the following analysis techniques: SEM/EDAX, XRD, TEM, metallography, thermogravimetry. The candidate does not need to be specialised in high temperature corrosion, the position is opened to PhD in metallurgy, chemistry, physics, materials science. French speaking is welcomed but not compulsory. Toulouse, the "pink city", is a very nice place in the French south-west with a lot of motivations to learn fast some basics of French language ! Subject: The work in Toulouse with Prof. Bernard Pieraggi concerns the role of interfaces in high temperature corrosion. This project is conducted as well on model materials and on superalloys used mainly for aeronautics applications (Toulouse is a centre for Space and Aeronautics Industries). The current study is the interfacial effects of reactive elements (REE) on the growth of oxide scales. It has been shown that Ca or Sr could retard the growth of NiO on nickel. The postdoc will conduce more experiments on this topic in order to clarify the role of these additions and will work on the modelisation of this phenomenon. Ref.: The role of interface dislocations and ledges as sources/sinks for point defects in scaling reactions, J.P.Hirth, B. Pieraggi, R.A.Rapp, Acta Metall. Mater., vol. 43, 3, pp. 1065-1073, 1995. Interfacial scaling reactions and the reactive element effect, B.Pieraggi, R.A.Rapp, Materials at high temperatures, vol. 12, 2-3, 1994. Chromia scale growth in alloy oxidation and the reactive element effect, B.Pieraggi, R.A.Rapp, Journal of the electrochemical society, vol. 140, 10, 1993. _________________________________________________________ Daniel Monceau lab. Met. Phys. ENSCT - URA 445 CNRS 118 route de Narbonne F-31 077 TOULOUSE FRANCE phone: (33) 61-17-56-61 fax: (33)61-17-56-00 _________________________________________________________ -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: monceau@oceane.cict.fr -- Original Sender From: Address: cict.fr@cict.fr 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 chemistry-request@www.ccl.net Fri Jan 26 06:37:22 1996 Received: from harfang.CC.UMontreal.CA for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id GAA12589; Fri, 26 Jan 1996 06:36:50 -0500 Received: from meds1.MEDCN.UMontreal.CA (meds1.MEDCN.UMontreal.CA [132.204.11.103]) by harfang.CC.UMontreal.CA with ESMTP id GAA20361 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 06:36:00 -0500 Received: from harfang.CC.UMontreal.CA by meds1.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id LAA02080; Fri, 26 Jan 1996 11:37:10 GMT Received: from www.ccl.net (www.ccl.net [128.146.36.5]) by harfang.CC.UMontreal.CA with ESMTP id GAA20358 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 06:35:53 -0500 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id GAA12395; Fri, 26 Jan 1996 06:12:21 -0500 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.10/950822.1) id GAA12226; Fri, 26 Jan 1996 06:00:05 -0500 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA18847; Fri, 26 Jan 96 11:59:53 +0100 X-Nupop-Charset: Swiss Date: Fri, 26 Jan 1996 13:00:36 +0100 (MET) From: "Hr Dr. S. Shapiro" X-Original-Sender: toukie@zui.unizh.ch Sender: Computational Chemistry List Reply-To: toukie@zui.unizh.ch Message-Id: <46836.toukie@zui.unizh.ch> To: chemistry@www.ccl.net Subject: CCL:? re molecular imaging Errors-To: ccl@www.ccl.net Precedence: bulk X-Caution: User has inserted an Explicit Reply-To Dear Colleagues; I am working with a Sybyl .mol2 file under DOS (file extension ".mol") which consists of a set of _disembodied_ (i.e., non-bonded) atoms floating in space. So far I have been unable to visualise this file using PCModel for Windows, HyperChem for Windows, or MOL2MOL for Windows, but I have succeeded in visualising it with RasMol 2.4 for Windows. I wish to obtain a stereo- scopic picture of this arrangement of atoms in space, but RasMol 2.4 only al- lows you to export in a limited number of _non-chemical_ formats such as ..bmp and .gif. Therefore, does anyone know of a mechanism whereby I might convert a .bmp or .gif image into one that can be visualised by PCModel, HyperChem, or MOL2MOL so that I can use one of these programmes to generate (and print) a stereoscopic image of this set of disembodied atoms? I might add that Babel for DOS rejects this .mol file consisting of disembodied atoms. Thanks in advance to all responders. Sincerely, S. Shapiro Zuerich toukie@zui.unizh.ch -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: toukie@zui.unizh.ch -- Original Sender From: Address: toukie@zui.unizh.ch 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 chemistry-request@www.ccl.net Fri Jan 26 08:52:24 1996 Received: from harfang.CC.UMontreal.CA for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id IAA13364; Fri, 26 Jan 1996 08:47:47 -0500 Received: from meds1.MEDCN.UMontreal.CA (meds1.MEDCN.UMontreal.CA [132.204.11.103]) by harfang.CC.UMontreal.CA with ESMTP id IAA22538 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 08:46:57 -0500 Received: from harfang.CC.UMontreal.CA by meds1.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id NAA03931; Fri, 26 Jan 1996 13:48:10 GMT Received: from www.ccl.net (www.ccl.net [128.146.36.5]) by harfang.CC.UMontreal.CA with ESMTP id IAA22534 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 08:46:52 -0500 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id IAA13124; Fri, 26 Jan 1996 08:24:40 -0500 Received: from nmr1.ioc.ac.ru for val@nmr1.ioc.ac.ru by www.ccl.net (8.6.10/950822.1) id IAA13042; Fri, 26 Jan 1996 08:16:12 -0500 Received: from [193.233.3.134] by nmr1.ioc.ac.ru with SMTP (WG7Jv1.07b+CWRU/BIOCv1.93) id AA10712 ; Fri, 26 Jan 96 16:15:48 MST Date: Fri, 26 Jan 96 16:15:16 +0300 From: "Valentin P Ananikov" Message-Id: <69965.val@nmr1.ioc.ac.ru> X-Minuet-Version: Minuet1.0_Beta_17A Reply-To: X-POPMail-Charset: IBM 8-Bit To: chemistry@www.ccl.net Subject: CCL:Metallocomplexes geomtry optimization Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk X-Caution: User has inserted an Explicit Reply-To Dear Netter, I am looking for some programs(for IBM PC) for geometry optimization of metallocomplexes with 'sigma' and 'pi' bonds: - [Me-CH=CHR(Hal)n] Hal=Cl,I; Me= platinum group metal (sigma vinyl complexes.) - [Me- - - C=C-C=C(Hal)n] ( pi complexes of platinum group metals with substituted dienes). Also I will be thankful to you if you let me know the references that contain X-ray data and Quantum chemistry results for complexes of that kind. Many thanks in advance. Regards, Valentin P.Avanikov Institute of Physical Organic & Coal Chemistry R. Luxembourg str.70 Ukraine e-mail: val@nmr1.ioc.ac.ru -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: val@nmr1.ioc.ac.ru -- Original Sender From: Address: val@nmr1.ioc.ac.ru 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 owner-chemistry@ccl.net Fri Jan 26 09:07:25 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 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 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 chemistry-request@www.ccl.net Fri Jan 26 11:52:27 1996 Received: from harfang.CC.UMontreal.CA for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id LAA16021; Fri, 26 Jan 1996 11:43:17 -0500 Received: from meds1.MEDCN.UMontreal.CA (meds1.MEDCN.UMontreal.CA [132.204.11.103]) by harfang.CC.UMontreal.CA with ESMTP id LAA29777 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 11:42:26 -0500 Received: from harfang.CC.UMontreal.CA by meds1.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id QAA13050; Fri, 26 Jan 1996 16:43:41 GMT Received: from www.ccl.net (www.ccl.net [128.146.36.5]) by harfang.CC.UMontreal.CA with ESMTP id LAA29773 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 11:42:22 -0500 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id LAA15301; Fri, 26 Jan 1996 11:03:07 -0500 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.10/950822.1) id KAA15023; Fri, 26 Jan 1996 10:47:10 -0500 From: Received: from rzurs3.unizh.ch by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA02390; Fri, 26 Jan 96 16:47:00 +0100 Received: by rzurs3.unizh.ch (AIX 3.2/UCB 5.64/4.03) id AA51378; Fri, 26 Jan 1996 15:45:23 +0100 Message-Id: <9601261445.AA51378@rzurs3.unizh.ch> Subject: CCL:Seeking RasMol FTP site To: chemistry@www.ccl.net Date: Fri, 26 Jan 1996 15:45:23 +0100 (MET) X-Mailer: ELM [version 2.4 PL24 PGP2] Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk Dear Colleagues, I am seeking an FTP site (not a WWW site) from which I might be able to download a copy of RasMol 2.6 (or else RasMol 2.5). If anyone can send me de- tails (FTP site address, subdirectory, file name), I would be most grateful. Sincerely, S. Shapiro Zuerich toukie@zui.unizh.ch -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: toukie@zui.unizh.ch -- Original Sender From: Address: toukie@zui.unizh.ch 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 chemistry-request@www.ccl.net Fri Jan 26 13:07:27 1996 Received: from harfang.CC.UMontreal.CA for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id NAA17136; Fri, 26 Jan 1996 13:05:23 -0500 Received: from meds1.MEDCN.UMontreal.CA (meds1.MEDCN.UMontreal.CA [132.204.11.103]) by harfang.CC.UMontreal.CA with ESMTP id NAA03631 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 13:04:32 -0500 Received: from harfang.CC.UMontreal.CA by meds1.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id SAA16065; Fri, 26 Jan 1996 18:05:44 GMT Received: from www.ccl.net (www.ccl.net [128.146.36.5]) by harfang.CC.UMontreal.CA with ESMTP id NAA03620 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 13:04:16 -0500 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id MAA16874; Fri, 26 Jan 1996 12:38:20 -0500 Received: from argus.cem.msu.edu for lawson@argus.cem.msu.edu by www.ccl.net (8.6.10/950822.1) id MAA16801; Fri, 26 Jan 1996 12:30:00 -0500 From: Received: from bohr.cem.msu.edu by argus.cem.msu.edu via ESMTP (950215.SGI.8.6.10/940406.SGI) for id MAA10241; Fri, 26 Jan 1996 12:30:34 -0500 Received: by bohr.cem.msu.edu (940816.SGI.8.6.9/) for chemistry@www.ccl.net id MAA26180; Fri, 26 Jan 1996 12:30:41 -0500 Date: Fri, 26 Jan 1996 12:30:41 -0500 Message-Id: <199601261730.MAA26180@bohr.cem.msu.edu> To: chemistry@www.ccl.net Subject: CCL:G:g92 quadrupole moments? Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk I would like to compare quadrupole moments computed by Gaussian92/DFT with moments computed by another code. Gaussian however, does not compute a non-traceable quadrupole moment for a homonuclear diatomic. (I believe some matrix rotation is required to give me a 'Buckingham type' traceless quadrupole, but I am not sure.) Is there anybody out there who knows how to transform 'g92' quadrupole moments to traceless quadrupole moments? Thanks Much! Dan Lawson lawson@bohr.cem.msu.edu -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: lawson@argus.cem.msu.edu -- Original Sender From: Address: lawson@argus.cem.msu.edu 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 chemistry-request@www.ccl.net Fri Jan 26 13:22:27 1996 Received: from harfang.CC.UMontreal.CA for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id NAA17189; Fri, 26 Jan 1996 13:09:17 -0500 Received: from meds1.MEDCN.UMontreal.CA (meds1.MEDCN.UMontreal.CA [132.204.11.103]) by harfang.CC.UMontreal.CA with ESMTP id NAA03771 (8.6.11/IDA-1.6); Fri, 26 Jan 1996 13:08:05 -0500 Received: from harfang.CC.UMontreal.CA by meds1.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id SAA16296; Fri, 26 Jan 1996 18:09:20 GMT Received: from www.ccl.net (www.ccl.net [128.146.36.5]) by harfang.CC.UMontreal.CA with ESMTP id NAA03766 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 13:08:01 -0500 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id MAA16799; Fri, 26 Jan 1996 12:29:52 -0500 Received: from volvo.wavefun.com for huang@mazda.wavefun.com by www.ccl.net (8.6.10/950822.1) id MAA16702; Fri, 26 Jan 1996 12:19:48 -0500 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for CHEMISTRY@www.ccl.net id AA04261; Fri, 26 Jan 96 09:20:03 -0800 Received: from mazda.wavefun.com(198.147.95.6) by volvo.wavefun.com via smap (V1.3) id sma004259; Fri Jan 26 09:19:56 1996 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:CHEMISTRY@www.ccl.net id AA20605; Fri, 26 Jan 96 09:19:24 -0800 From: "Wayne Huang" Message-Id: <9601260919.ZM20603@mazda.wavefun.com> Date: Fri, 26 Jan 1996 09:19:23 -0800 In-Reply-To: "John R. Nash" "CCL:From one structure to another" (Jan 24, 1:14pm) References: <199601241914.NAA130594@audumla.students.wisc.edu> Reply-To: huang@wavefun.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: "John R. Nash" , CHEMISTRY@www.ccl.net Subject: CCL:G:From one structure to another Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk X-Caution: User has inserted an Explicit Reply-To On Jan 24, 1:14pm, John R. Nash wrote: > Subject: CCL:From one structure to another > I am seeking a utility that will take as input the cartesian coordinates > of compounds A and B and generate x number of intermediate structures in > between the two by interpolation (i.e. morphing from one structure to the > other). I know that some packages will do this sort of thing for "linear > synchronous transit" calculations, but I need the input files for a > computation where this is not included. (The molecule is way too big for > GAUSSIAN... could the program perhaps be convinced to calculate the > coordinates w/o running the qm calculation on them?) This seems like an > simple enough utility to write, but my guess is that it must have been done > by someone... Seems you want to a dynamic constrain exercise. Coordinate driving which allow one to generate a list of molecule by promoting its geometrical parameters (can be more than one simultaneously or in sequence) of a single structure, but this requires optimization of some sort, at least MM. --Wayne -- +---------------------------------------------------------------------+ | Wayne Huang, Ph.D. | 18401 Von Karman, Suite 370 | | Computational Chemist | Irvine, California 92715 | | Wavefunction, Inc. | (714)955-2120 Fax: (714)955-2118 | | huang@wavefun.com | World Wide Web: http://wavefun.com | +---------------------------------------------------------------------+ -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: huang@mazda.wavefun.com -- Original Sender From: Address: huang@mazda.wavefun.com 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 chemistry-request@www.ccl.net Fri Jan 26 14:22:28 1996 Received: from harfang.CC.UMontreal.CA for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id OAA18218; Fri, 26 Jan 1996 14:12:01 -0500 Received: from meds1.MEDCN.UMontreal.CA (meds1.MEDCN.UMontreal.CA [132.204.11.103]) by harfang.CC.UMontreal.CA with ESMTP id OAA06180 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 14:10:59 -0500 Received: from harfang.CC.UMontreal.CA by meds1.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id TAA20432; Fri, 26 Jan 1996 19:12:14 GMT Received: from www.ccl.net (www.ccl.net [128.146.36.5]) by harfang.CC.UMontreal.CA with ESMTP id OAA06169 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 14:10:50 -0500 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id NAA17883; Fri, 26 Jan 1996 13:56:08 -0500 Received: from helix.nih.gov for gmercier@helix.nih.gov by www.ccl.net (8.6.10/950822.1) id NAA17690; Fri, 26 Jan 1996 13:44:41 -0500 Received: from [128.231.66.71] (ppc71.od.nih.gov [128.231.66.71]) by helix.nih.gov (8.6.12/8.6.12) with SMTP id NAA17878 for ; Fri, 26 Jan 1996 13:44:38 -0500 Message-Id: Date: Fri, 26 Jan 1996 14:56:33 -0500 To: chemistry@www.ccl.net From: gmercier@helix.nih.gov (Gustavo A. Mercier, Jr.) Subject: CCL:ADF 2.x on IRIX4.05f R4K Installation Problems Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk Hi! I am trying to test ADF 2.x on an old system. Unfortunately, I had problems installing the software and running the samples. After some playing around with options, I was able to compile the software, but I get a cryptic ADF error message. Unfortunately, the machine is stand - alone, and before I try some maneuvers to give the ADF people access, I would like to know: Has anybody had any success mounting and running ADF 2.x on an SGI R4000 running IRIX4.05f? Thanks Gus Mercier, Jr NIH - LDRR gmercier@helix.nih.gov -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: gmercier@helix.nih.gov -- Original Sender From: Address: gmercier@helix.nih.gov 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 boyd@chem.iupui.edu Fri Jan 26 14:37:28 1996 Received: from indyvax.iupui.edu for boyd@chem.iupui.edu by www.ccl.net (8.6.10/950822.1) id OAA18603; Fri, 26 Jan 1996 14:35:57 -0500 Return-receipt-to: Boyd Received: from macgw.chem.iupui.edu by INDYVAX.IUPUI.EDU (PMDF V5.0-5 #5862) id <01I0GX02I5B400FJUI@INDYVAX.IUPUI.EDU> for chemistry@www.ccl.net; Fri, 26 Jan 1996 14:35:54 -0500 Date: Fri, 26 Jan 1996 14:34:20 -0500 From: Boyd Subject: FREE BOOK SET To: OSC CCL Message-id: <01I0GX02IY8Y00FJUI@INDYVAX.IUPUI.EDU> Content-transfer-encoding: 7BIT Fellow Computational Chemists, This is a final reminder for winning a free set of "Reviews in Computational Chemistry" books for your library. As offered in our Jan. 17 CCL posting, we will donate a set (Volumes 1-7, 1990-1995) to a departmental, college, or university library. This offer is open to all countries. To enter on behalf of your library, send an email to: boyd@chem.iupui.edu. In the Subject line put the words FREE BOOKS. In the body of the e-mail put the name of your librarian and their postal address, one sentence about why your library could use these books, and your own email address and affiliation. The winner will be picked by random and announced over the OSC CCL. All entries must be received before February 1, 1996. So as not to overwork our mail system, please do not enter more than once. (There may be phase interference and cancellation!) We recommend looking at http://chem.iupui.edu/~boyd/rcc.html for other information about the books. Dr. Kenny B. Lipkowitz & Dr. Donald B. Boyd Indiana University-Purdue University at Indianapolis Co-Editors, "Reviews in Computational Chemistry" From chemistry-request@www.ccl.net Fri Jan 26 14:37:33 1996 Received: from harfang.CC.UMontreal.CA for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id OAA18589; Fri, 26 Jan 1996 14:33:39 -0500 Received: from meds1.MEDCN.UMontreal.CA (meds1.MEDCN.UMontreal.CA [132.204.11.103]) by harfang.CC.UMontreal.CA with ESMTP id LAA28784 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 11:22:33 -0500 Received: from harfang.CC.UMontreal.CA by meds1.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id QAA11742; Fri, 26 Jan 1996 16:23:48 GMT Received: from www.ccl.net (www.ccl.net [128.146.36.5]) by harfang.CC.UMontreal.CA with ESMTP id LAA28775 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 11:22:27 -0500 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id KAA15186; Fri, 26 Jan 1996 10:56:10 -0500 Received: from mallard.duc.auburn.edu for newhoir@duc.auburn.edu by www.ccl.net (8.6.10/950822.1) id KAA15040; Fri, 26 Jan 1996 10:48:04 -0500 Received: by mallard.duc.auburn.edu (5.x/SMI-SVR4) id AA06546; Fri, 26 Jan 1996 09:48:00 -0600 Date: Fri, 26 Jan 1996 09:48:00 -0600 From: newhoir@duc.auburn.edu (Irene Newhouse) Message-Id: <9601261548.AA06546@mallard.duc.auburn.edu> To: chemistry@www.ccl.net Subject: CCL:G:G94: IRC output in internals? Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk The output from IRC computations done with Gaussian 94 rev C.3 seems to be in cartesian coordinates even if I do the IRC in internals. I'd much rather have the output in internal coordinates: is this possible? Thanks for your help! Irene Newhouse newhoir@mail.auburn.edu -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: newhoir@duc.auburn.edu -- Original Sender From: Address: newhoir@duc.auburn.edu 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 chemistry-request@www.ccl.net Fri Jan 26 14:37:36 1996 Received: from harfang.CC.UMontreal.CA for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id OAA18581; Fri, 26 Jan 1996 14:33:07 -0500 Received: from meds1.MEDCN.UMontreal.CA (meds1.MEDCN.UMontreal.CA [132.204.11.103]) by harfang.CC.UMontreal.CA with ESMTP id LAA00060 (8.6.11/IDA-1.6); Fri, 26 Jan 1996 11:48:32 -0500 Received: from harfang.CC.UMontreal.CA by meds1.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id QAA13132; Fri, 26 Jan 1996 16:49:47 GMT Received: from www.ccl.net (www.ccl.net [128.146.36.5]) by harfang.CC.UMontreal.CA with ESMTP id LAA00054 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 11:48:26 -0500 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id LAA15374; Fri, 26 Jan 1996 11:06:59 -0500 Received: from camsci.com for jsb2@camsci.com by www.ccl.net (8.6.10/950822.1) id KAA14995; Fri, 26 Jan 1996 10:44:10 -0500 From: Date: Fri, 26 Jan 96 10:43:07 EST Received: by camsci.com (4.1/3.1.090690-Cambridge Scientific Computing) id AA27120; Fri, 26 Jan 96 10:43:07 EST Message-Id: <9601261543.AA27120@camsci.com> To: chemistry@www.ccl.net, toukie@zui.unizh.ch Subject: CCL:? re molecular imaging Cc: CHMINF-L@IUBVM.UCS.INDIANA.EDU Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk > I am working with a Sybyl .mol2 file under DOS (file extension ".mol") >which consists of a set of _disembodied_ (i.e., non-bonded) atoms floating in >space. So far I have been unable to visualise this file using PCModel for >Windows, HyperChem for Windows, or MOL2MOL for Windows, but I have succeeded >in visualising it with RasMol 2.4 for Windows. I wish to obtain a stereo- >scopic picture of this arrangement of atoms in space, but RasMol 2.4 only al- >lows you to export in a limited number of _non-chemical_ formats such as > ..bmp and .gif. Therefore, does anyone know of a mechanism whereby I might >convert a .bmp or .gif image into one that can be visualised by PCModel, >HyperChem, or MOL2MOL so that I can use one of these programmes to generate >(and print) a stereoscopic image of this set of disembodied atoms? Wouldn't it be simpler to just load it into Chem3D directly and create the stereoscopic views there, rather than going through all the other file formats? Chem3D will add the bonds back in for you, too if you want. Information about Chem3D (including demo versions for Mac and Windows) is available from http://www.camsoft.cmm Jonathan Brecher CambridgeSoft Corporation jsb@camsoft.com -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: jsb2@camsci.com -- Original Sender From: Address: jsb2@camsci.com 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 chemistry-request@www.ccl.net Fri Jan 26 15:22:33 1996 Received: from harfang.CC.UMontreal.CA for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id PAA19079; Fri, 26 Jan 1996 15:07:43 -0500 Received: from meds1.MEDCN.UMontreal.CA (meds1.MEDCN.UMontreal.CA [132.204.11.103]) by harfang.CC.UMontreal.CA with ESMTP id PAA08575 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 15:06:48 -0500 Received: from harfang.CC.UMontreal.CA by meds1.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id UAA23144; Fri, 26 Jan 1996 20:08:02 GMT Received: from www.ccl.net (www.ccl.net [128.146.36.5]) by harfang.CC.UMontreal.CA with ESMTP id PAA08565 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 15:06:43 -0500 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id OAA18825; Fri, 26 Jan 1996 14:53:31 -0500 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.10/950822.1) id OAA18757; Fri, 26 Jan 1996 14:47:48 -0500 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.1/8.7.1) id OAA08182 for chemistry@www.ccl.net; Fri, 26 Jan 1996 14:47:41 -0500 (EST) Date: Fri, 26 Jan 1996 14:47:41 -0500 (EST) From: "E. Lewars" Message-Id: <199601261947.OAA08182@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: CCL:G:STEREO PICTURE FROM CARTESIANS Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk 1996 Jan 26 Hello, There was a recent query about getting a stereo image from a set of "disembodied atoms", evidently Cartesians with no connectivity (no bonds specified). The program MolWin, for IBM compatible PC's, will accept Cartesians and give a mono or stereo picture. It will also accept Gaussian output (G92; G94 output may have to be modified) and, for freq jobs, animate vibrations. The pictures can be exported to WordPerfect, annotated and printed. MolWin was written by Dr Pavel Ganelin of the Catholic University of America, 48ganelin@cua.edu It should be obtainable from oak.oakland.edu/simtel/win3/chem/molwin23.zip E. Lewars ==== -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: elewars@alchemy.chem.utoronto.ca -- Original Sender From: Address: elewars@alchemy.chem.utoronto.ca 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 chemistry-request@www.ccl.net Fri Jan 26 17:22:31 1996 Received: from harfang.CC.UMontreal.CA for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id RAA20766; Fri, 26 Jan 1996 17:08:56 -0500 Received: from meds1.MEDCN.UMontreal.CA (meds1.MEDCN.UMontreal.CA [132.204.11.103]) by harfang.CC.UMontreal.CA with ESMTP id RAA13894 (8.6.11/IDA-1.6); Fri, 26 Jan 1996 17:07:54 -0500 Received: from harfang.CC.UMontreal.CA by meds1.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id WAA01839; Fri, 26 Jan 1996 22:09:05 GMT Received: from www.ccl.net (www.ccl.net [128.146.36.5]) by harfang.CC.UMontreal.CA with ESMTP id RAA13891 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 17:07:41 -0500 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id QAA20670; Fri, 26 Jan 1996 16:56:49 -0500 Received: from azure.CCIT.Arizona.EDU for MOMOT@CCIT.ARIZONA.EDU by www.ccl.net (8.6.10/950822.1) id QAA20560; Fri, 26 Jan 1996 16:47:58 -0500 Received: from CCIT.ARIZONA.EDU by CCIT.ARIZONA.EDU (PMDF V5.0-5 #2381) id <01I0GX6FQG0G9QVCUV@CCIT.ARIZONA.EDU>; Fri, 26 Jan 1996 14:41:02 -0700 (MST) Date: Fri, 26 Jan 1996 14:41:02 -0700 (MST) From: momot@CCIT.ARIZONA.EDU Subject: CCL:Mobility paradox In-reply-to: <9601180918.AA20536@otto.mpimf-heidelberg.mpg.de> To: Eberhard von Kitzing Cc: Computational Chemistry List Message-id: X-Envelope-to: CHEMISTRY@www.ccl.net Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk > left hand side and right hand side > > cations jC(left) = + F mu1 E cC and jC(right) = + F mu2 E cC > > anions jA(left) = - F mu2 E cA and jA(right) = - F mu1 E cA > > where F is Faraday's constant. But this implies jC(left) != jC(right) and > jA(left) != jA(right) which violates the particle conservation law. I would For jC(left), it's cC on the right side For jC(right), cC on the left As the current is turned on, the "right" and "left" concentrations change until the two fluxes become equal (i.e. stationary situation is established). (I am sure it's more complex in reality, you may never actually reach the steady state). -- Konstantin Momot -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: MOMOT@CCIT.ARIZONA.EDU -- Original Sender From: Address: momot@CCIT.ARIZONA.EDU 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 chemistry-request@www.ccl.net Fri Jan 26 19:37:32 1996 Received: from harfang.CC.UMontreal.CA for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id TAA22176; Fri, 26 Jan 1996 19:29:32 -0500 Received: from meds1.MEDCN.UMontreal.CA (meds1.MEDCN.UMontreal.CA [132.204.11.103]) by harfang.CC.UMontreal.CA with ESMTP id PAA09525 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 15:24:20 -0500 Received: from harfang.CC.UMontreal.CA by meds1.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id UAA24198; Fri, 26 Jan 1996 20:25:34 GMT Received: from www.ccl.net (www.ccl.net [128.146.36.5]) by harfang.CC.UMontreal.CA with ESMTP id PAA09517 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 15:24:06 -0500 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id PAA19125; Fri, 26 Jan 1996 15:09:27 -0500 Received: from www.hyper.com for vuckovic@hyper.com by www.ccl.net (8.6.10/950822.1) id OAA18936; Fri, 26 Jan 1996 14:59:01 -0500 Received: (from vuckovic@localhost) by www.hyper.com (8.6.12/8.6.12) id PAA17702 for chemistry@www.ccl.net; Fri, 26 Jan 1996 15:05:45 -0500 From: Dragan Vuckovic Message-Id: <199601262005.PAA17702@www.hyper.com> Subject: CCL:HyperChem Workshop - California To: chemistry@www.ccl.net Date: Fri, 26 Jan 1996 15:05:43 -0500 (EST) X-Mailer: ELM [version 2.4 PL24] Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk Hypercube, Inc. presents an Introductory HyperChem Workshop on Computational Chemistry April 10 -12, 1996 Ready Serve Computer Center Santa Clara, California, USA HyperChem is like any other powerful tool: the more you know about it, the more you get out of working with it. For those who wish to learn more about the methods of molecular modeling and computational chemistry, about the ways of working with HyperChem, and about the range of problems you can now tackle on a PC, Hypercube, Inc. (the developers of HyperChem) offer an intensive three-day introductory workshop on molecular modeling with HyperChem. The workshop is pragmatic and application-oriented and makes no assumption of previous computational chemistry experience. Workshop Objectives The workshop will introduce you to techniques for working efficiently with HyperChem and other Hypercube's products, provide a pragmatic user's guide to the scientific methods behind HyperChem, and include many hands-on exercises based on practical molecular modeling problems. Workshop Outline Day 1. Morning: Overview of Computational Chemistry Techniques; HyperChem Graphical Interface Afternoon: Molecular Mechanics Methods Laboratory session Day 2. Morning: Approximate and Semiempirical Molecular Orbital Methods; Ab initio Molecular Orbital Methods Afternoon: Frontier Orbital Theory: Examining Molecular Reactivity; Laboratory session Day 3. Morning: Molecular Dynamics; Molecular Spectroscopy; QSAR/Group Contribution Methods Afternoon: Laboratory session (optional) Costs and Venue The cost for the three-day course is $995 US (Academic and Government discount price is $795 US). For early registration (before March 15) the price is $925 US ($725 US - academic). This covers the cost of course materials, coffee, lunches, and a PC to work on for the duration of the course (each participant will have his/her own machine). The number of participants is limited, so that extensive interaction with the workshop instructors is possible. Bring your own problems to work on during the course! The course will be held at the Ready Serve Computer Center, 5201 Great America Parkway, Suite 355, Santa Clara, California, USA. A map and a list of nearby reasonably-priced hotels will be sent to all participants upon registration. The participants are expected to make their own travel and accommodation arrangements. Registration To register for the Workshop, please complete the form and return as soon as possible 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 Registration Form HyperChem Workshop on Computational Chemistry Santa Clara, California, USA April 10-12, 1996 Please reserve ____ spaces for the above workshop. NAME _______________________________________________________ ORGANIZATION _______________________________________________ POSITION ___________________________________________________ ADDRESS FOR CORRESPONDENCE ____________________________________________________________ ____________________________________________________________ ____________________________________________________________ TEL. NO. _______________________ FAX NO. ___________________ Fees payable in advance: I enclose a check for $__________ US Please make your check payable to Hypercube, Inc. Please invoice me: Purchase Order Number __________________ VISA Card No: ____________________________ Exp. Date: _________ Cardholder: ________________________________ Amount $________US SIGNATURE _____________________________ DATE ___________________ *Cancellation: If a participant cancels on or before March 27th (two weeks before the workshop), 50% of the workshop fee will be refunded. There will be no refunds for cancellations received after March 27, 1995. ___________________________________________________________________ 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 -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: vuckovic@hyper.com -- Original Sender From: Address: vuckovic@hyper.com 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 chemistry-request@www.ccl.net Fri Jan 26 19:52:31 1996 Received: from harfang.CC.UMontreal.CA for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id TAA22280; Fri, 26 Jan 1996 19:43:28 -0500 Received: from meds1.MEDCN.UMontreal.CA (meds1.MEDCN.UMontreal.CA [132.204.11.103]) by harfang.CC.UMontreal.CA with ESMTP id TAA19895 (8.6.11/IDA-1.6); Fri, 26 Jan 1996 19:41:59 -0500 Received: from harfang.CC.UMontreal.CA by meds1.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id AAA05658; Sat, 27 Jan 1996 00:43:11 GMT Received: from www.ccl.net (www.ccl.net [128.146.36.5]) by harfang.CC.UMontreal.CA with ESMTP id TAA19857 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 19:41:52 -0500 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id TAA22044; Fri, 26 Jan 1996 19:25:16 -0500 Received: from optima.cs.arizona.edu for local%rupley.UUCP@cs.arizona.edu by www.ccl.net (8.6.10/950822.1) id TAA21985; Fri, 26 Jan 1996 19:15:08 -0500 Received: from rupley.UUCP by optima.cs.arizona.edu (5.65c/15) via UUCP id AA15382; Fri, 26 Jan 1996 17:15:05 MST Received: by rupley.UUCP (911016.SGI/911001.SGI) for arizona!www.ccl.net!CHEMISTRY id AA28454; Sat, 27 Jan 96 00:14:56 GMT Date: Sat, 27 Jan 96 00:14:56 GMT From: local%rupley.UUCP@cs.arizona.edu (John Rupley) Message-Id: <9601270014.AA28454@rupley.UUCP> To: CHEMISTRY@www.ccl.net Subject: CCL:Online doccument defining polypeptide dihedrals Cc: rupley!local@cs.arizona.edu Reply-To: rupley@cs.arizona.edu Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk X-Caution: User has inserted an Explicit Reply-To I would be grateful if someone would point me to preferably online documentation giving the standards (IUPAC?) specifying the atom quadruples for polypeptide dihedrals. This is not entirely trivial, since the order of the atoms defines positive rotation of the dihedral, and for some (e.g. proline N-CD or CD-N?) the choice is not clear. Thanks, John Rupley rupley@cs.arizona.edu -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: local%rupley.UUCP@cs.arizona.edu -- Original Sender From: Address: local%rupley.UUCP@cs.arizona.edu 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 chemistry-request@www.ccl.net Fri Jan 26 22:22:33 1996 Received: from harfang.CC.UMontreal.CA for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id WAA24486; Fri, 26 Jan 1996 22:13:57 -0500 Received: from meds1.MEDCN.UMontreal.CA (meds1.MEDCN.UMontreal.CA [132.204.11.103]) by harfang.CC.UMontreal.CA with ESMTP id VAA21862 (8.6.11/IDA-1.6); Fri, 26 Jan 1996 21:18:24 -0500 Received: from harfang.CC.UMontreal.CA by meds1.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id CAA06651; Sat, 27 Jan 1996 02:19:40 GMT Received: from www.ccl.net (www.ccl.net [128.146.36.5]) by harfang.CC.UMontreal.CA with ESMTP id VAA21858 (8.6.11/IDA-1.6 for ); Fri, 26 Jan 1996 21:18:21 -0500 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id UAA22771; Fri, 26 Jan 1996 20:55:55 -0500 Received: from vp.netgate.net for wally@CompChem.com by www.ccl.net (8.6.10/950822.1) id UAA22605; Fri, 26 Jan 1996 20:38:23 -0500 Received: from p90 (d15.netgate.net [205.214.160.47]) by vp.netgate.net (8.6.12/8.6.9) with SMTP id RAA28348; Fri, 26 Jan 1996 17:56:10 -0800 Message-Id: <2.2.32.19960127013753.002e35e4@ng.netgate.net> X-Sender: wally@ng.netgate.net X-Mailer: Windows Eudora Pro Version 2.2 (32) Date: Fri, 26 Jan 1996 17:37:53 -0800 To: rupley@cs.arizona.edu From: "Walter E. Reiher III" Subject: CCL:Online doccument defining polypeptide dihedrals Cc: CHEMISTRY@www.ccl.net Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk At 12:14 AM 1/27/96 GMT, John Rupley wrote: > >I would be grateful if someone would point me to preferably online >documentation giving the standards (IUPAC?) specifying the atom >quadruples for polypeptide dihedrals. This is not entirely trivial, >since the order of the atoms defines positive rotation of the dihedral, >and for some (e.g. proline N-CD or CD-N?) the choice is not clear. I'd also like to know about an online version of this, but the standard paper version is of course: IUPAC-IUB Commission on Biochemical Nomenclature. Abbreviations and Symbols for the Description of the Conformation of Polypeptide Chains Biochemistry 9, 3471-3479 (1970) also published in J Biol Chem 245, 6489 (1970) J Mol Biol 52, 1 (1970) Wally ======================================================================== Walter E. Reiher III, Ph.D. Wally@CompChem.com CompChem Innovations Consulting in computational chemsitry P.O. Box 61056 voice 408-720-0240 Sunnyvale, CA 94088 fax 408-720-0378 -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: wally@CompChem.com -- Original Sender From: Address: wally@CompChem.com 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