From jkl@ccl.net Mon Oct 25 01:51:53 1993 Received: from krakow.ccl.net for jkl@ccl.net by www.ccl.net (8.6.1/930601.1506) id BAA17734; Mon, 25 Oct 1993 01:50:44 -0400 From: Jan Labanowski Received: from localhost for jkl@ccl.net by krakow.ccl.net (8.6.1/920428.1525) id BAA25234; Mon, 25 Oct 1993 01:50:42 -0400 Date: Mon, 25 Oct 1993 01:50:42 -0400 Message-Id: <199310250550.BAA25234@krakow.ccl.net> To: chemistry@ccl.net Subject: List restored Cc: jkl@ccl.net Dear Subscribers, The Computational Chemistry List is restored. Unfortunately, it took much more time than expected. The archives, and other services do not work yet as expected. The anonymous ftp on www.ccl.net will be moved to www.ccl.net. The OSCPOST@ccl.net service for retrieving files will be replaced by MAILSERV@ccl.net (you may send a message HELP to it, but I still need to look at some details). Searching of chemistry archives is not yet ready. They will in a few days. It is time for me to sleep, since I barely see... Jan Labanowski jkl@ccl.net From jkl@ccl.net Mon Oct 25 07:04:54 1993 Received: from gandalf.ciam.unibo.it for ivan@gandalf.ciam.unibo.it by www.ccl.net (8.6.1/930601.1506) id GAA19434; Mon, 25 Oct 1993 06:21:40 -0400 Received: by gandalf.ciam.unibo.it (AIX 3.2/UCB 5.64/4.03) id AA11172; Mon, 25 Oct 1993 09:20:40 +0100 Date: Mon, 25 Oct 1993 09:20:40 +0100 From: ivan@gandalf.ciam.unibo.it (Ivan Rossi) Message-Id: <9310250820.AA11172@gandalf.ciam.unibo.it> To: chemistry@ccl.net Subject: Khoros Dear netters, recently I heard about a public domain graphic software called Khoros which seems roughly equivalent to packages like AVS, Data Explorer, etc. Everyone who used it told me that it runs on a lot of platforms, it is a very good software and it is free. Has anyone here experience in molecular graphics using Khoros? It is really useful to a computational chemist ? Ivan Ivan Rossi | Theoretical Organic Chemistry Group | Department of Chemistry "G. Ciamician" | EXPERT : someone who avoids all University of Bologna | Via Selmi 2, 40126 Bologna - Italy | the little errors, going straight | Tel. ++39-51-259495 | towards the catastrophe Fax ++39-51-259456 | e-mail ivan@gandalf.ciam.unibo.it | From jkl@ccl.net Mon Oct 25 08:04:55 1993 Received: from bernina.ethz.ch for yama@molbio.ethz.ch by www.ccl.net (8.6.1/930601.1506) id HAA19829; Mon, 25 Oct 1993 07:58:22 -0400 Received: from odin by bernina.ethz.ch with SMTP inbound id <18468-0@bernina.ethz.ch>; Mon, 25 Oct 1993 12:58:17 +0100 From: Bernhard Anton Pabsch Received: from noldi by odin id AA08179; Mon, 25 Oct 93 12:58:01 +0100 Date: Mon, 25 Oct 93 12:59:07 +0100 Message-Id: <9310251159.AA22997@noldi> Received: by noldi id AA22997; Mon, 25 Oct 93 12:59:07 +0100 To: CHEMISTRY@ccl.net, rachelle@picard.niehs.nih.gov Subject: GRASP summary This is the summary of answers concerning a request on GRASP. Thanks for your reply. This mailexploder is a nice thing! The original question: Dear netters, in the last two days on the LATSIS Symposium in Zurich on Horizons in Structural Biology I learnd about the program GRASP from W Hendrickson. Is that program publicly available by ftp? The answers: From: carlos@extreme.bio.cornell.edu (Carlos Faerman) I was under the impression that GRASP is by Anthony Nicholls and Barry Honig... This program is to carry out electrostatic calculations and display the results. If this is the program you care about it costs $500 (at least that was the price for academics). If you need more help let me know carlos h. faerman From: OSELLA@ch.unito.it (The Mad (Al)Chemists Group) You can find the Public Domain version of Grasp directly in Suisse: try nic.switch.ch in the directory software/msdos/simtel20/animation The file should be PDGRASP.ZIP (or something like this). Carlo -------------------------------------------------------------------------------- Dr. Carlo Nervi, Dipartimento di Chimica Inorganica, Chimica Fisica e Chimica dei Materiali, via P. Giuria 7, 10125 Torino, ITALIA. Internet: osella@silver.ch.unito.it -------------------------------------------------------------------------------- From: shenkin@still3.chem.columbia.edu (Peter Shenkin) GRASP is not from W. Hendrickson. It is from Barry Honig's lab, and was written by Anthony Nicholls, "nicholls@cuhhca.hhmi.columiba.edu". You should contact him for further info. -P. ************************f*u*cn*rd*ths*u*cn*gt*a*gd*jb************************ Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ., New York, NY 10027; shenkin@still3.chem.columbia.edu; (212) 854-5143 ********************** Wagner, Beame, Screvane in '93! ********************** From: Max Vasquez Hello, the program GRASP was originally described by Nicholls et al. in Proteins 11, 282 (1991). This paper came from Barry Honig's group, like Hendrickson, also at Columbia University. I do not know if one can get this program free by ftp, but I doubt it. They may have included some information about availability in the above reference. I would be interested in finding out about that too. Best wishes, ======================================== Max Vasquez, PhD Protein Design Labs, Inc. 2375 Garcia Ave. Mountain View CA 94043 Phone (415) 903 3744 FAX (415) 903 3730 e-Mail wk01189 @ worldlink.com ======================================== From: krystek@alcor.bms.com (Stanley Krystek) GRASP is available from Anthony Nicholls at Columbia at E-mail nicholls@cuhhca.hhmi.columbia.edu. There is a small charge for the program but i can say it is well worth it. Anthony also responds to E-mail questions wich is a help in getting started. stan Stanley R. Krystek, Jr., Ph.D. Bristol-Myers Squibb Pharmaceutical Research Institute Department of Macromolecular Modeling P.O. Box 4000, Room H.3812, Princeton, N.J. 08543-4000 (609) 252-4100 FAX: (609) 252-6030 INTERNET: krystek@bms.com From: youkha@biosym.com (Philippe Youkharibache) The program GRASP was written by Anthony Nicholls at Columbia. Although he is in the same department of Wayne Hendrickson, Wayne is just a user of GRASP. Anthony has set up an anonymous ftp account with 20 or so grasp pictures, with notes illustrating what the program can do, as well as an demo version. Its at cumbnd.bioc.columbia.edu (128.59.96.103). Anthony Nicholls can be reached at nicholls@cuhhca.hhmi.columbia.edu ************************************************************************** Dr. Philippe Youkharibache e-mail: youkha@biosym.com Biosym Technologies Inc. 9685 Scranton Road tel: (619) 546 5562 San Diego, CA 92121 fax: (619) 458 0136 ************************************************************************** From jkl@ccl.net Mon Oct 25 09:04:55 1993 Received: from monte.br.RohmHaas.Com for rs0thp@RohmHaas.Com by www.ccl.net (8.6.1/930601.1506) id IAA20317; Mon, 25 Oct 1993 08:49:03 -0400 Received: by monte.br.RohmHaas.Com (AIX 3.2/UCB 5.64/4.03) id AA16189; Mon, 25 Oct 1993 08:48:01 -0400 From: rs0thp@RohmHaas.Com (Dr. Tom Pierce) Message-Id: <9310251248.AA16189@monte.br.RohmHaas.Com> Subject: Re: ACD Gopher and Group 4 Fax Compression To: chemistry@ccl.net Date: Mon, 25 Oct 1993 08:48:00 +22305350 (EDT) Cc: h.rzepa@ic.ac.uk (Henry Rzepa) In-Reply-To: <9310221729.AA21803@cscmgb.cc.ic.ac.uk> from "Henry Rzepa" at Oct 22, 93 05:28:26 pm X-Mailer: ELM [version 2.4 PL13] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 688 Previously, Henry Rzepa wrote: > > I am having difficulty reading the TIFF images > on the ACS Gopher. I have tried both > JPEG Viewer 3.0 and GIFConverter 2.3.1 on > a Macintosh, but neither supports the G4 Fax > compression. > Can anyone help? Dear Folks, I use xv on a IBM unix system ( xv freeware for viewing graphics files available on archie) and it works with the ACS gopher *.tif files. Perhaps there is a Macintosh version of xv somewhere? -- Sincerely, Thomas Pierce, Internet Address: THPierce@RohmHaas.Com Observation - Network Computing is Computer Slavery. Official Disclaimer:"The opinions expressed are those of the writer and not the Rohm and Haas Company." From jkl@ccl.net Mon Oct 25 10:04:56 1993 Received: from ac.dal.ca for JKONG@ac.dal.ca by www.ccl.net (8.6.1/930601.1506) id JAA20755; Mon, 25 Oct 1993 09:43:19 -0400 From: Received: from AC.DAL.CA by AC.DAL.CA (PMDF V4.2-14 #2545) id <01H4IYZ67OA8000TXH@AC.DAL.CA>; Mon, 25 Oct 1993 10:42:17 -0300 Date: Mon, 25 Oct 1993 10:42:16 -0300 Subject: Summary of transfering software to PC To: chemistry@ccl.net Message-id: <01H4IYZ6A33M000TXH@AC.DAL.CA> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT My original question is: > Can one install a unix system like linux on a 486 and then run > quantum chemistry software like G92? > I thought so in principle but I am not sure. It is interesting to see that there are quite a few people trying to do heavy stuff on PC. From their replies, I got the impression that you can run large applications on PC with unix but you need big memory(16MB), big disk space, and perhaps fast disk drives. Also you have to transfer the codes to C since there is no fortran compilor for Linux yet(There is a tool for that purpose though. See replies). Thank you all who responsed. Following are the replies: **************************************************** Jing- Yes, that is possible, but G92 will need huge resources when on a UNIX based computer. However, there is a PC version of G92 available, and will use the PC in less demanding manner. Virtually, Edward Wolpert > Would you please tell me how much resorce is needed? Do you know anyone > who has done that kind of thing? I know G92 has a Window version, but my > friend does not want to pay. Besides, it needs too much memory(mim. 16MB). > I guess that is because Windows does not support virtual memeroy or paging. Actually, the Window version needs less memory then G92/UNIX. If you run it with less memory available, then it will be very slow, and on a 486, it's bad enough. Too much paging can increase time from 200%-1000% easily. I run G90, and have gotten it to use 200MB for G90's temp and it's own paging. The computer that runs it has over 512MB of hardware memory, and I use between 16-30MB of it for my program. To run G92, you need at _least_ 16 MB of memory to get it going effectively, and 300MB of diskspace (minimum). Virtual memory is bad on any personal computer since most read/write access time is quite slow, causing the program to move at a crawl. PC's were not made to handle such calculations. Even a 50Mhz 486 is too slow. I would imagin that for small molecules, with small basis sets, you can use 8MB of real memory. You would save time and sweat if you upgraded the PC to 16MB (32MB if you can) and use g92 windows. G92 (UNIX) compiling on Linux is not a garentee. Also, don't for get the Linux uses a lot of computer memory and diskspace for itself. See what other people say, but I don't suggest you do this. Virtually, Edward Wolpert Actually, the eariler versions (IMO) where not as well programed, so they ate memory, and took a longer time to run then the latest. Gaussian sent us a newsletter that compared older versions of their program, and G92 is the fastest. I believe that if They could have writen the program for a PC five years ago, they would have. (Like mopac is found on almost any platform) Ab initio calculations are so huge though, so it is hard to see it be usefull on a PC. You might try to experiment with GAMES (I think it's public domain, I'm not sure though since I don't use it) or eariler versions of HONDO to see how well they can preform on your best PC platform. (Hondo should compile alright on any ANSI C compiler, but may need 'fixing') I've never tried it, but it seems like a week's worth of work to me. Virtually, Edward Wolpert --------------------------------------------------------------------- |wolpert@osti.slip.utk.edu | | |wolpert@neon.chem.utk.edu | (Sign on Doctor's Office Door...) | |wolpert@lead.chem.utk.edu | | |wolpert@utkux1.utk.edu | Dr. Godot's Office | |wolpert@utkvx.utk.edu | Be Back in Five | |wolpert@martha.utcc.utk.edu | | |wolpe... you get the picture | | -------------------------------------------------------------------- ********************************************* =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Nikita Matsunaga Wilhelm Hall #402 Department of Chemistry (515)-294-9925 Iowa State University (515)-294-5204 fax Ames, IA 50011-3111 =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= X-Mailer: ELM [version 2.4beta PL7] Content-Type: text Content-Length: 914 Jing, The biggest problem with Linux is that there is no fortran available. A rumor has it that GNU is in the process of releasing one. So, as it is one has to use "FtoC" program to convert fortran to C, which could be a pain. I cannot speak for Gaussian 92, but our code, GAMESS, would be able to run on Linux. A friend of mine has put Linux on a 486 machine, and has converted a part of GAMESS, relatively minor, to be able to have a smooth conversion with "ftoc" program available at AT&T Bell Lab. He told me that he's been running for a year and had no problem yet so far. Obviously, the hardest part is to run ftoc program to convert GAMESS into C program. If you are interested let me know. And, if you or your friend is interested in obtaining GAMESS, which is a program with no charge, please contact Mike Schmidt, mike@si.fi.ameslab.gov. Nikita Jing, I finally found the configuration that my friend, John Montgomery of United Technologies Research Center, suggested. A suitable machine for running GAMESS will have 1) 486DX, minimum 8Mb memory, 16Mb better 2) IDE disk drive, 200 Mb or larger (some SCSI controllers will work but installation is easier with IDE drives) 3) ET4000 video card and mutifrequency monitor, if you want to run graphics package supplied with GAMESS. They, i.e. molecular plot, plotting orbitals, electrostatic potential, etc., run under X. Thus far, I've installed Linux on a 486 machine from Gateway. It was relatively painless, and will be installing X and GAMESS, whenever I find some time. Nikita ******************************************************************** Jing, We have not tried such a configuration but I am not confident that it would work. The requirements on the Fortran compiler are quite large and the interfacbetween C and Fortran is quite often tricky. Your friend can ask more detailed questions on help@gaussian.com. Doug Fox Director of Technical Support help@gaussian.com ************************************************************************* Hello: Sure you can, we have ported GAMESS to FreeBSD and it runs without problems. For a better performance I would sugest your friend setup a PC with: 486 50 MHz, 16 M ram (minimum), SCSI disks. Regards Pedro ********************************************************************************* Yes, he could/ He must (?) compile his program for Linux enviroment and alll go on!. I am currently involwed with MOPAC 6.0 for Linux. If I or my friends find something interesting I wikk send a message to Computational Chemistry list. Wojciech Galazka From: Wojciech Galazka Here's my answer to your questions: * I have neither MOPAC 6.0 nor any other ab initio (generally quantum) program in C. I have some ones but all they are in FORTRAN. Explanation of this situation is simply: - many good numeric libs and algoritms are still in FORTRAN, - FORTRAN is a too primitive language to do something wrong instead of C, - almost all quantum chemists still write in FORTRAN. I was told it was possible to convert FORTRAN files to C using f2c program from anonymous ftp at research@att.com (password: netlib), but I/O routines in FORTRAN sources seemed to cause problems during translation. The f2c is available in source codes so you may test it yourself. * I heard there will be gnu (GNU ?) FORTRAN compiler available, this will be the best solution for FORTRAN codes of quantum programs. * I had to uninstall my Linux from my 386DX 33MHz 8MB RAM IDE 250MB HDD , but it worked. I think for large programs such as MOPAC it is neccessary to have at least 8MB RAM, fast 486 33MHz machine and at least 50MB (fifty) free disk space to get results in reasonable time. This configuration should be enough for MOPAC with 100 heave and 100 light atoms. * I did not test Linux with SCSI drivers. Look for Linux FAQ for more information. Hope this help. //////////////////////////////////////////////////////////// // // // Wojciech Galazka // // Computer Center // // Chemistry Department, University of Warsaw // // Pasteura 1, 02-093 Warsaw, Poland // // // // wgalazka@zoolook.chem.uw.edu.pl // //////////////////////////////////////////////////////////// *************************************************************** From: m10!frisch@uunet.uu.net (Michael Frisch) Subject: RE: Q: 486+unix+g92 works? In-reply-to: uunet!ac.dal.ca!JKONG, Mon, 18 Oct 1993 12:23:01 -0300 A version of Gaussian 92 is available which runs on 486 systems under Microsoft Windows. Contact info@gaussian.com for details. Making the unix workstation version of G92 run under linux is conceivable but would probably be a fair amount of work, which no one has attempted yet. Mike Frisch ------- ************************************************************** From: MA NGAI LING I don't think it is legal to port G92 to 486 if there is nothing available right now. If he doesn't want to use Windows, I don't think there is one yet. However, has he considered using GAMESS? GAMESS is free and you may be able to port it to Linux. Ida -- ***************************************************** From: Andreas Windemuth > Can one install a unix system like linux on a 486 and then run > quantum chemistry software like G92? > I thought so in principle but I am not sure. I have a 586-PC from ALR that I run NEXTSTEP on. I have run molecular dynamics at 2-3 times the speed of an SGI 220 GTX. You need either "f2c" or a third party fortran compiler (Absoft sells one for NEXTSTEP) to run chemistry software. I have never had trouble using f2c (which is free) to run fortran code on unix (NeXT) machines. For example, X-plor was successfully compiled this way on a NeXT some time ago. I am very happy with the ALR/NEXTSTEP combination, I get 2/3 the computing power of an SGI Indigo 2 for a small fraction of the price ($6000). And NEXTSTEP is a great general productivity environment. Andreas Windemuth +-------------------------------------------------------------------- |Columbia University, Dept. of Biochemistry and Biophysics, BB-221 |630 West 168th St. | tel: (212)-305-6884, fax: 6926, NeXTmail |New York, NY 10032 | email: windemut@cumbne.bioc.columbia.edu +-------------------------------------------------------------------- **************************************************************** From jkl@ccl.net Mon Oct 25 12:06:33 1993 Received: from denmark.den.mmc.com for hogue@denmark.den.mmc.com by www.ccl.net (8.6.1/930601.1506) id LAA22186; Mon, 25 Oct 1993 11:45:57 -0400 Received: by denmark.den.mmc.com (4.1/1.34.a) id AA01785; Mon, 25 Oct 93 09:45:25 MDT Date: Mon, 25 Oct 93 09:45:25 MDT From: hogue@denmark.den.mmc.com (Pat Hogue 1-2183) Message-Id: <9310251545.AA01785@denmark.den.mmc.com> To: chemistry@ccl.net Subject: New book Hi folks: From time to time requests are posted for good elementary textx books on molecular orbital theory. I would like to endorse the new book by Yves Jean and Francois Volatron (Jeremy Burdett translator) "An Introduction to Molecular Orbitals" Oxford University Press (1993). The last section (section 3) deals with the geometry and reactivity of molecules. Pat Hogue From jkl@ccl.net Mon Oct 25 12:08:55 1993 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.1/930601.1506) id LAA22290; Mon, 25 Oct 1993 11:55:05 -0400 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA12649 (5.65c/IDA-1.4.4 for ); Mon, 25 Oct 1993 16:54:43 +0100 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA01082; Mon, 25 Oct 93 16:52:31 +0100 Date: Mon, 25 Oct 1993 16:49:00 +0100 (MET) From: Patrick Bultinck Subject: GAMESS OUTPUT/INSTALL To: CHEMISTRY@ccl.net Cc: Patrick.Bultinck@rug.ac.be Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1096 Dear Netters, I am using Gamess for my ab initio study of different aspects of macrocyclic chemistry. I would like to know if somebody has got a way of writing the output of the PLTORB program to a postscript file for easy printing on a PS printer. (as is possible with the DENDIF program) This would be very helpful if again somebody is asking me for a pictural representation of a certain MO for a major molecule. Second I would like to know if somebody uses Gamess on a SUN SPARCcenter 1000 (Op.Sys. Solaris2.2). I can only get a limited amount of disk space for my calculations on the University network, and I would like to know how much disk space is required to perform calculations (both direct and not-direct SCF). If anyone replies please state what calculation you have performed and how large the produced files were (both the kept-ones (the output) + the removed ones (integral files etc.)), and how much memory is required for the program. Thanks, Patrick Bultinck, University of Ghent Belgium (yes, somewhere between Spain and Sweden...) e-mail : Patrick.Bultinck@rug.ac.be