From chp1aa@surrey.ac.uk Thu May 27 04:48:22 1993 From: Mr Andrew D Allen Message-Id: <9305270750.AA04163@central.surrey.ac.uk> Subject: RE: Archie To: chemistry@ccl.net Date: Thu, 27 May 93 8:50:30 BST My 2 penneth worth, Archie is fairly versitile and as has been mentioned allows you to see if any system has the file you want. There are many Archie servers, and you'll have to experiment to find which ones are most useful in terms of speed and accessibility. To access an Archie site simple telnet to the site with the server and login as archie, a help facillity is provided. One recommendation is to set the sortby option to hostname:- set sortby hostname This ensures that when you then go system hopping to check out the files, you don't have to go back to a site you have already visited. Saves time in the long run. Another option is to use Veronica. This is available if you have access to a gopher server. Since I find gopher so much easier to use I now prefer to look for files by using Veronica. The main advantage of Veronica and the other gopher wigits is that any compressed files can be uncompressed by downloading the appropriate decompression software. Each file has a note attached saying how to extract the files. Happy hopping, Andy. From chp1aa@surrey.ac.uk Thu May 27 05:02:11 1993 From: Mr Andrew D Allen Message-Id: <9305270834.AA28349@central.surrey.ac.uk> Subject: Polymer Modelling To: chemistry@ccl.net Date: Thu, 27 May 93 9:34:03 BST Dear All, I have a colleague who is interested in modelling network formation in highly crosslinked polymer systems. We would like to know if anyone has tried to model these types of systems in any way shape or form. The system that we want to deal with consists of two monomers with different functionalities. Our initial thoughts have been to model the network on a simple grid upon which the monomers could be placed. Monomer-monomer reaction would be permitted only for adjacent vertices occupied by different monomers. By randomly shifting the free monomers and fragments formed by reaction of monomers (oligomers) we would hope to simulate the diffusion of the different reactive species throughout the polymer mixture. By repeating the above procedure and applying the conditions for monomer reaction it should be possible to gain a very simplified model for the development of the polymer network. This approach has much in common with 'Monte-Carlo' type calculations and we were wondering if anybody out there had used any packages / Programs which facilitate the development of such models; perhaps simplifying the task of setting parameters and limits for the model and storing fragment data. Any help or guidance would be appreciated very much indeed. Thanks in advance Andy From P84031@BARILVM.BIU.AC.IL Thu May 27 05:48:28 1993 Message-Id: <199305270902.AA01250@oscsunb.ccl.net> Date: Thu, 27 May 93 11:56:49 IDT From: "Dr. Pinchas Aped" Subject: A Program to Predict Crystal Structure To: CHEMISTRY@ccl.net Dear Netters: I am looking for a program to calculate/predict the "best" (lowest in energy or highest in density, within a defined potential) crystal arrangement of organic molecules. The important point: For the molecules of interest, no crystallographic data, such as point group, unit cell dimensions etc., is available. Any help will be greatly appreciated. Pinchas Aped ------------------------------------------------------------------------ Dr. Pinchas Aped Tel.: (+972-3) 531-8634 Department of Chemistry FAX : (+972-3) 535-1250 Bar-Ilan University E-Mail: P84031@BARILVM (bitnet) 52900 Ramat-Gan, ISRAEL aped@gefen.cc.biu.ac.il ------------------------------------------------------------------------ From LONCHARICH_RICHARD_J@Lilly.com Mon May 27 02:56:34 1993 Date: 27 May 1993 07:56:34 -0500 (EST) From: Rick Loncharich Subject: Re: Diels-Alder transition states To: chemistry@ccl.net Message-Id: <01GYNUXMPQ4Y8WVYK1@INET.D48.LILLY.COM> REPLY TO: >I'm trying to lend a hand to a real pot-boiling organic chemist who's >interested in modeling Diels-Alder transition states. He was hoping >to use Mopac, but we've found that with both AM1 and MNDO the diene >ends up a good 7A from the dieneophile (system is ethylene and a >substituted Cp). Is this kind of behavior something I should have >expected? If so, recommendations for, say, a review paper accessible >to the non-theorist would be appreciated! Thanks. >-- >David J. Heisterberg (djh@ccl.net) Gee, it's so beautiful, I gotta >The Ohio Supercomputer Center give somebody a sock in the jaw. >Columbus, Ohio -- Little Skippy (Percy Crosby) We have published several articles on Diels-Alder transition states calculated with AM1 and ab initio basis sets. The AM1 calculations of cyclopentadiene with ethylene and cyclopentadiene with acrylonitrile revealed geometries quite similar to the ab initio results, however energetics differed. See for example "Substituent Effects and Transition Structures for Diels-Alder Reactions of Butadiene and Cyclopentadiene with Cyanoalkanes" Houk, K.N. et al. JACS, 1989, 111, 9172- 9176. The article is tailored to the organic bench chemist! From: LONCHARICH RICHARD J (MCVAX0::RX82788) To: FOREIGN TRANSPORT ADDRESSEE (MCDEV1::IN%"chemistry@ccl.net") From states@wucs1.wustl.edu Thu May 27 04:30:24 1993 Message-Id: <9305271527.AA07503@wucs1.wustl.edu> Date: Thu, 27 May 1993 10:30:24 -0600 To: CHEMISTRY@ccl.net From: states@wucs1.wustl.edu Subject: Computational Biology mailing list? >From: Ilya Logunov >Date: Wed, 26 May 93 17:40:56 -0500 >To: CHEMISTRY@ccl.net >Subject: Computational Biology mailing list? > > Does anybody know about the existence of any mailing list in >Computational Biology similar to this Computational Chemistry mailing >list? Several of the bionet news groups on Usenet are devoted to computational biology, software, and related issues. Start with bionet.general, bionet.software, and bionet.biology.computational. Larry Hunter maintains a directory of computational biologist at the National Library of Medicine which is accessible by anonymous ftp: host: ncbi.nlm.nih.gov login: anonymous password: your e-mail address directory: /pub/aimb-db You can also look at the University of Houston sever maintained by Dan Davison on the host "evolution.bchs.uh.edu" David States From pbays@saintmarys.edu Thu May 27 15:26:42 1993 Date: Thu, 27 May 1993 10:26:42 +0500 () From: Phil Bays Subject: Hp Hardware To: Chemistry Message-Id: I am interested in knowing what commonly used computational chemistry packages are available for the HP series of workstations. I know that Spartan is, and that Tripos products are not. What about AVS, MOPAC, GAUSSIAN? Are there other packages that you know of which run on HP, particularly those which might interest a biochemist? Phil Bays pbays@saintmarys.edu From vincent@retina.chem.psu.edu Thu May 27 07:28:29 1993 Date: Thu, 27 May 93 11:28:29 -0400 From: vincent@retina.chem.psu.edu (Jim Vincent) Message-Id: <9305271528.AA29997@retina.chem.psu.edu> To: CHEMISTRY@ccl.net Subject: RE: Archie Telnet to an archie server is probably the least desirable method of access. One should get an archie client. There are many available. These are promoted when one tries to telnet to an archie server but can't get in because there are too may users. If you don't have any archie client, telnet (once) to an archie server and note the locations of the clients it lists as available. Xarchie is an x based archie client that can be found in many places, also. Jim From mwd@carina.cray.com Thu May 27 05:37:46 1993 From: mwd@carina.cray.com (Mark Dalton) Message-Id: <9305271537.AA13144@calamity> Subject: Re: ARCHIE / gopher To: chemistry@ccl.net Date: Thu, 27 May 93 10:37:46 CDT Gopher is another option that incorporates archie. This also has many other handy options. Like on-line literature searches, access to other gopher servers, If you have other questions feel free to contact me directly. or If you have questions or comments, you can get in contact with the Gopher development team by sending e-mail to: gopher@boombox.micro.umn.edu There is also a USENET news discussion group called comp.infosystems.gopher where Internet Gopher is discussed. Gopher Info This is a heavily edited version of the Gopher FAQ intended to give people just starting with gopher enough information to get a client and jump into Gopher-space - a complete version can be obtained as described below. Common Questions and Answers about the Internet Gopher, a client/server protocol for making a world wide information service, with many implementations. Posted to comp.infosystems.gopher, comp.answers, and news.answers every two weeks. The most recent version of this FAQ can be gotten through gopher, or via anonymous ftp: pit-manager.mit.edu:/pub/usenet/news.answers/gopher-faq Those without FTP access should send e-mail to mail-server@rtfm.mit.edu with "send usenet/news.answers/finding-sources" in the body to find out how to do FTP by e-mail. ------------------------------------------------------------------- List of questions in the Gopher FAQ: Q0: What is Gopher? Q1: Where can I get Gopher software? Q2: What do I need to access Gopher? Q3: Where are there publicly available logins for Gopher? Q4: Who Develops Gopher Software? Q5: What is the relationship between Gopher and (WAIS, WWW, ftp)? Q6: What is veronica? ------------------------------------------------------------------- Q0: What is Gopher? A0: The Internet Gopher client/server provides a distributed information delivery system around which a world/campus-wide information system (CWIS) can readily be constructed. While providing a delivery vehicle for local information, Gopher facilitates access to other Gopher and information servers throughout the world. ------------------------------------------------------------------- Q1: Where can I get Gopher software? A1: via anonymous ftp to boombox.micro.umn.edu. Look in the directory /pub/gopher -------------------------------------------------------------------- Q2: What do I need to access Gopher? A2: You will need a gopher "client" program that runs on your local PC or workstation There are clients for the following systems. The directory following the name is the location of the client on the anonymous ftp site boombox.micro.umn.edu (134.84.132.2) in the directory /pub/gopher. Unix Curses & Emacs : /pub/gopher/Unix/gopher1.12.tar.Z Xwindows (athena) : /pub/gopher/Unix/xgopher1.2.tar.Z Xwindows (Motif) : /pub/gopher/Unix/moog Macintosh Hypercard : /pub/gopher/Macintosh-TurboGopher/old-versions * Macintosh Application : /pub/gopher/Macintosh-TurboGopher * DOS w/Clarkson Driver : /pub/gopher/PC_client/ NeXTstep : /pub/gopher/NeXT/ VM/CMS : /pub/gopher/Rice_CMS/ or /pub/gopher/VieGOPHER/ VMS : /pub/gopher/VMS/ OS/2 2.0 : /pub/gopher/os2/ MVS/XA : /pub/gopher/mvs/ Many other clients and servers have been developed by others, the following is an attempt at a comprehensive list. A Macintosh Application, "MacGopher". ftp.cc.utah.edu:/pub/gopher/Macintosh * Another Macintosh application, "GopherApp". ftp.bio.indiana.edu:/util/gopher/gopherapp * A port of the UNIX curses client for DOS with PC/TCP oac.hsc.uth.tmc.edu:/public/dos/misc/dosgopher.exe A port of the UNIX curses client for PC-NFS bcm.tmc.edu:/nfs/gopher.exe A beta version of the PC Gopher client for Novell's LAN Workplace for DOS lennon.itn.med.umich.edu:/dos/gopher A VMS DECwindows client for use with Wollongong or UCX job.acs.ohio-state.edu:XGOPHER_CLIENT.SHARE * Note: these Macintosh clients require MacTCP. Most of the above clients can also be fetched via a gopher client Most of the above clients can also be fetched via a gopher client itself. Put the following on a gopher server: Type=1 Host=boombox.micro.umn.edu Port=70 Path= Name=Gopher Software Distribution. Or point your gopher client at boombox.micro.umn.edu, port 70 and look in the gopher directory. There are also a number of public telnet login sites available. The University of Minnesota operates one on the machine "consultant.micro.umn.edu" (134.84.132.4) See Q3 for more information about this. It is recommended that you run the client software instead of logging into the public telnet login sites. A client uses the custom features of the local machine (mouse, scroll bars, etc.) A local client is also faster. --------------------------------------------------------------------- Q3: Where are there publicly available logins (ie places to telnet to in order to get a taste of gopher) for Gopher? A3: Here is a short list, use the site closest to you to minimize network lag. Telnet Public Logins: Hostname IP# Login Area ------------------------- --------------- ------ ------------- consultant.micro.umn.edu 134.84.132.4 gopher North America gopher.uiuc.edu 128.174.33.160 gopher North America panda.uiowa.edu 128.255.40.201 panda North America gopher.sunet.se 192.36.125.2 gopher Europe info.anu.edu.au 150.203.84.20 info Australia gopher.chalmers.se 129.16.221.40 gopher Sweden tolten.puc.cl 146.155.1.16 gopher South America ecnet.ec 157.100.45.2 gopher Ecuador tn3270 Public Logins: Hostname IP# Login Area ------------------------- --------------- ------ ------------- pubinfo.ais.umn.edu 128.101.109.1 -none- North America It is recommended that you run the client software instead of logging into the public login sites. A client uses the custom features of the local machine (mouse, scroll bars, etc.) --------------------------------------------------------------------- Q5: Who Develops Gopher Software? A5: Gopher was originally developed in April 1991 by the University of Minnesota Microcomputer, Workstation, Networks Center to help our campus find answers to their computer questions. It has since grown into a full-fledged World Wide Information System used by a large number of sites in the world. Many people have contributed to the project, too numerous to count. The people behind the much of the gopher software can be reached via e-mail at gopher@boombox.micro.umn.edu, or via paper mail: Internet Gopher Developers 100 Union St. SE #190 Minneapolis, MN 55455 USA Or via FAX at: +1 (612) 625-6817 --------------------------------------------------------------------- Q6: What is the relationship between Gopher and (WAIS, WWW, ftp)? A6: Gopher is intimately intertwined with these two other systems. As shipped the Unix gopher server has the capability to: - Search local WAIS indices. - Query remote WAIS servers and funnel the results to gopher clients. - Query remote ftp sites and funnel the results to gopher clients. - Be queried by WWW (World Wide Web) clients (either using built in gopher querying or using native http querying. ------------------------------------------------------------------- Q7: What is veronica? A7: veronica: Very Easy Rodent-Oriented Net-wide Index to Computerized Archives. veronica offers a keyword search of most gopher-server menu titles in the entire gopher web. As archie is to ftp archives, veronica is to gopherspace. A veronica search produces a menu of gopher items, each of which is a direct pointer to a gopher data source. Because veronica is accessed through a gopher client, it is easy to use, and gives access to all types of data supported by the gopher protocol. To try veronica, select it from the "Other Gophers" menu on Minnesota's gopher server, or point your gopher at: Name=veronica (search menu items in most of GopherSpace) Type=1 Port=70 Port=70 Path=1/veronica Host=futique.scs.unr.edu -- _____________________________________________________________________________ |Mark Dalton | AUG-GCU-AGA-AAG H | |Cray Research, Inc. | M A R K | | |Eagan, MN 55121 | CH3-S-CH2-CH2-C-COOH | |Internet: mwd@cray.com | | | |(612)683-3035 | NH2 | ----------------------------------------------------------------------------- From lim@rani.chem.yale.edu Thu May 27 10:07:01 1993 From: Dongchul Lim Message-Id: <9305271807.AA05581@rani.chem.yale.edu> Subject: RE: Archie To: chemistry@ccl.net (Computational Chemistry) Date: Thu, 27 May 93 14:07:01 EDT Mr Andrew D Allen writes: > My 2 penneth worth, > Archie is fairly versitile and as has been mentioned allows you to see > if any system has the file you want. There are many Archie servers, and you'll > have to experiment to find which ones are most useful in terms of speed and > accessibility. To access an Archie site simple telnet to the site with the > server and login as archie, a help facillity is provided. One recommendation > is to set the sortby option to hostname:- [...] Direct telneting to archie servers is not always easy, since the number of maximum users at one time is limited to a couple of hundred (?). Try to install an archie client on your system. This gives a much faster access to archie servers. Then you probably could do something like this on your command prompt. % archie archie -DCL From kjalkan@ncsa.uiuc.edu Thu May 27 10:23:00 1993 Date: Thu, 27 May 93 15:23:00 CDT From: kjalkan@ncsa.uiuc.edu ( Karl James Jalkanen) Message-Id: <9305272023.AA23735@troon.ncsa.uiuc.edu> To: CHEMISTRY@ccl.net Subject: NEW "GREEN CARD" RULES PROPOSED TO RELIEVE SCIENTIST SHORTAGE Not to all computational chemists in US (this may affect us all). You may want to contact you congressman before 5/30/93? |> 3. NEW "GREEN CARD" RULES PROPOSED TO RELIEVE SCIENTIST SHORTAGE. |> No, really! Physics is not on the list, but the Labor Department |> wants to make it easier for employers to hire foreign scientists |> and engineers in certain fields, including chemistry, computer |> science and materials engineering. The proposed rules, published |> in the March 19 Federal register, would automatically certify |> aliens in these fields for permanent residence in states said to |> have a shortage. Employers would not have to advertise openings |> to Americans before hiring aliens. How are shortages determined? |> >From the number of "labor certifications" filed by employers. The |> comment period on the proposed rules is extended to 30 May 1993. Question for everyone? Is there really a shortage of computational chemists/chemists in general? NOTE the important point: Employers would not have to advertise openings |> to Americans before hiring aliens. karl From rks2@crux2.cit.cornell.edu Thu May 27 12:38:55 1993 Message-Id: <9305272038.AA03576@crux2.cit.cornell.edu> To: CHEMISTRY@ccl.net From: rks2@cornell.edu (Rebecca K. Schmidt) Subject: Conferences in Australia? Date: Thu, 27 May 93 16:38:55 -0400 Dear Chem-Netters, I'm interested in attending conferences/symposia/workshops about computational chemistry and applied statistical mechanics in Australia or New Zealand within the next year. Please send me notices if you know of any. Thanks! Cheers, Rebecca Schmidt ****************************************************************************** * Rebecca Schmidt phone: (607) 255-2006 * 120 Stocking Hall FAX: (607) 254-4868 * Cornell University Email: rks2@cornell.edu * Ithaca, NY 14853 ****************************************************************************** From system@alchemy.chem.utoronto.ca Thu May 27 12:48:12 1993 Date: Thu, 27 May 93 16:48:12 -0400 From: system@alchemy.chem.utoronto.ca (System Admin (Mike Peterson)) Message-Id: <9305272048.AA26302@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: Re: HP hardware G92 runs fine on HP-UX 8.07, and those binaries run on 9.01, but not at the best performance possible on the new 7x5 workstations. Recompiled G92 on 9.01 does not run properly; cause under investigation by Gaussian. I have a verified MOPAC 6.0 on 8.07, but you need source for the BSD F77/I77/U77 libraries to make it work since it makes a lot of calls to those routines. Some of those routines are supplied with 9.01, but I haven't upgraded yet to find out if all the right ones are there, and after the G92 problems (and others), I'm not hurrying. I can give you a MOPAC 6 executable that will work, but you'll have to use the same path names I have, and trust that I haven't put anything nasty in there. I've also got DRAW and DENSITY working, with no major problems. The Quantum Chemistry Literature DataBase (QCLDB), with all the ab initio QC literature from the past 2 decades, from Hosoya/Morokuma/Yamabe/Ohno also works fine. Mike. U/Toronto Chemistry System Manager (and part-time quantum chemist) E-mail: system@alchemy.chem.utoronto.ca Tel: (416)978-7094 Fax: (416)978-8775 From jaeric@mtcamm.monsanto.com Thu May 27 11:01:44 1993 From: Jon A. Erickson Message-Id: <9305272101.AA03297@mtcamm.monsanto.com> Subject: UV-Vis simulation... To: chemistry@ccl.net (OSU Comp. Chem. List) Date: Thu, 27 May 93 16:01:44 CDT Dear Netters, Does anyone know of any work involving the simulation/prediction of UV-Vis spectra? Any code or references would be of help. Thanx in advance for the help. -- ################################################################ # Jon Erickson e-mail: jaeric@mtcamm.monsanto.com # # Monsanto Company, U3E phone: (314) 694-1511 # # 800 N. Lindbergh Blvd. # # St. Louis MO, 63167 # # # # What is a magician but a practising theorist? # # -- Obi-Wan Kenobi # ################################################################ From theresa@si.fi.ameslab.gov Thu May 27 14:34:47 1993 From: theresa@si.fi.ameslab.gov (Theresa Windus) Message-Id: <9305280034.AA27789@si.fi.ameslab.gov> Subject: Re: HP hardware To: chemistry@ccl.net () Date: Thu, 27 May 93 19:34:47 CDT Hi! GAMESS (an ab initio program) is available on the HP platform. Contact Mike Schmidt at mike@si.fi.ameslab.gov. This program is available free of charge. Theresa Windus Department of Chemistry Iowa State University Ames, IA 50011 e-mail: theresa@si.fi.ameslab.gov From rhn900@anusf.anu.edu.au Fri May 28 06:57:53 1993 From: Ross Nobes Message-Id: <199305280200.AA17169@anusf.anu.edu.au> Subject: Re: HP hardware To: system@alchemy.chem.utoronto.ca.chemistry (System Admin (Mike Peterson)) Date: Fri, 28 May 93 11:57:53 EST System Admin (Mike Peterson) writes: > > G92 runs fine on HP-UX 8.07, and those binaries run on 9.01, but not > at the best performance possible on the new 7x5 workstations. > Recompiled G92 on 9.01 does not run properly; cause under investigation > by Gaussian. > Gaussian 92 does run properly on HP 7x5 workstations under HP-UX 9.01 provided that patch PHSS_2191 has been applied to libvec.a. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Ross Nobes * * Academic Consultant * * Supercomputer Facility Phone: + 61 6 249 4154 / 4161 * * Australian National University Fax: + 61 6 247 3425 * * Canberra, ACT 0200 * * Australia E-mail: R.Nobes@anu.edu.au * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * From raman@bioc01.uthscsa.edu Thu May 27 16:03:11 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9305280203.AA02767@bioc01.uthscsa.edu> Subject: ARCHIE... To: chemistry@ccl.net Date: Thu, 27 May 1993 21:03:11 -0500 (CDT) Chuck If you have access to a UNIX workstation and X windows then you might want to consider "Xarchie" which has a nice interface and facilitates searching! There are many sites that carry the Xarchie client. -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** All Science is either Physics or stamp collecting -E.Rutherford ****************************************************************************** From raman@bioc01.uthscsa.edu Thu May 27 16:18:16 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9305280218.AA02789@bioc01.uthscsa.edu> Subject: Computational Biology - Gopher To: chemistry@ccl.net Date: Thu, 27 May 1993 21:18:16 -0500 (CDT) Dear Netters There is a GOPHER server devoted mainly to various aspects of Computational Biology and includes different protein and nucleic acid databases, software, etc. and can be accessed if you have a GOPHER client installed on your system: type "gopher merlot.welch.jhu.edu" and follow the instructions. This server is located at Johns Hopkins Univ. Yet another GOPHER server with a lot of computational features of interest to biologists and covers most of Europe is located in Heidelberg. You can access the same also via standalone GOPHER client: type "gopher ftp.embl-heidelberg.de" and follow the menu! The contents of the latter are mirrored in some of the sites in the U.S. including "fly.bio.indiana.edu". Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** All Science is either Physics or stamp collecting -E.Rutherford ******************************************************************************