From chemistry-request@www.ccl.net Wed Feb 24 04:08:17 1999 Received: from euler.central.cranfield.ac.uk (euler.central.cranfield.ac.uk [138.250.48.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA16093 Wed, 24 Feb 1999 04:08:16 -0500 (EST) Received: from cael-test.cael.cranfield.ac.uk ([138.250.75.1] helo=btmodelling) by euler.central.cranfield.ac.uk with smtp (Exim 1.92 #2) for chemistry@www.ccl.net id 10FaIh-00017Q-00; Wed, 24 Feb 1999 09:08:15 +0000 Message-Id: <3.0.3.32.19990224090345.0091b320@mailboxes.ccc.cranfield.ac.uk> X-Sender: bi0100@mailboxes.ccc.cranfield.ac.uk X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Wed, 24 Feb 1999 09:03:45 +0000 To: chemistry@www.ccl.net From: Richard M Day Subject: Simon Brocklehurst Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi, I lost the original EMAIL regarding Simon Brocklehurst, he is now working at Cambridge Antibody Technology Regards, Richard Day +44 1234 750111 x3563 From chemistry-request@www.ccl.net Wed Feb 24 05:24:59 1999 Received: from swan2.uspnet.usp.br (swan2.uspnet.usp.br [143.107.253.69]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA16407 Wed, 24 Feb 1999 05:24:55 -0500 (EST) Received: from ligquim ([143.107.194.89]) by swan2.uspnet.usp.br (8.9.1a/8.9.1) with SMTP id HAA04205 for ; Wed, 24 Feb 1999 07:21:59 -0300 (EST) Message-ID: <000201be5fdf$9a9738a0$0100005a@ligquim.ffclrp.usp.br> From: "Sergio Emanuel Galembeck" To: "CCL mail list" Subject: Termochemistry of radicals Date: Tue, 23 Feb 1999 17:52:25 -0300 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Content-Transfer-Encoding: 7bit Dear Netters, What is the best method to calculate energies of reactions involving radicals? Is compound methods like CBS-Q as good choice? Thanks a lot, Sergio From chemistry-request@www.ccl.net Wed Feb 24 07:50:26 1999 Received: from lgsx01.lg.ehu.es (lgsx01.lg.ehu.es [158.227.2.34]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA16977 Wed, 24 Feb 1999 07:50:24 -0500 (EST) Received: from lgdx04.lg.ehu.es (lgdx04.lg.ehu.es [158.227.1.36]) by lgsx01.lg.ehu.es (8.8.5/8.8.5) with SMTP id NAA12236 for ; Wed, 24 Feb 1999 13:51:27 +0100 (MET) Date: Wed, 24 Feb 1999 13:50:13 +0100 (MET) From: Pablo Vitoria Garcia To: ccl Subject: SUMMARY: Information about TopMoD program Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Thanks a lot to Wai-to Chan, Nathaniel Malcolm and Jean-Francois Paul for their replies. It seems that TopMoD was developed by Noury, Krokidis, Fuster, Silvi and Savin, and two possible contact addresses are: Xenophon.Krokidis@lct.jussieu.fr silvi@lct.jussieu.fr Thank you very much again Pablo -------------------------------------------------------------------------------- Pablo Vitoria Garcia Departamento de Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado 644, E-48080 Bilbao SPAIN e-mail: qibvigap@lg.ehu.es Phone: +34 94 6012000 Ext. 5529 -------------------------------------------------------------------------------- From chemistry-request@www.ccl.net Wed Feb 24 09:37:28 1999 Received: from iris.inc.bme.hu (iris.inc.bme.hu [152.66.63.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA18705 Wed, 24 Feb 1999 09:37:24 -0500 (EST) Received: from localhost (dino@localhost) by iris.inc.bme.hu (8.9.1/8.9.1) with ESMTP id PAA23254; Wed, 24 Feb 1999 15:36:56 +0100 (BUD) Date: Wed, 24 Feb 1999 15:36:56 +0100 From: Szieberth Denes To: Sergio Emanuel Galembeck cc: CCL mail list Subject: Re: CCL:Termochemistry of radicals In-Reply-To: <000201be5fdf$9a9738a0$0100005a@ligquim.ffclrp.usp.br> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Dear Netters, > > What is the best method to calculate energies > of reactions involving radicals? Is compound > methods like CBS-Q as good choice? > You can find a comparison of different model chemistries in: Ochterski, Petersson, Wiberg : J. Am. Chem. Soc. 1995, 117, 11299-11308 or you can use some not so computationally demanding approaches described in e.g.: Sana, Nguyen: CPL 1992 196(3,4) 390 Denes Szieberth dino@iris.inc.bme.hu From chemistry-request@www.ccl.net Wed Feb 24 10:38:23 1999 Received: from neon.ch.pwr.wroc.pl (neon.ch.pwr.wroc.pl [156.17.2.212]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA19223 Wed, 24 Feb 1999 10:38:11 -0500 (EST) Received: from neon.ch.pwr.wroc.pl (localhost [127.0.0.1]) by neon.ch.pwr.wroc.pl (980427.SGI.8.8.8/970903.SGI.AUTOCF) via SMTP id QAA13839 for ; Wed, 24 Feb 1999 16:36:20 +0100 (MET) Sender: jola@neon.ch.pwr.wroc.pl Message-ID: <36D41C73.41C6@neon.ch.pwr.wroc.pl> Date: Wed, 24 Feb 1999 16:36:19 +0100 From: Jolanta Grembecka Organization: Wroclaw University of Technology X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: ONIOM Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I would like to use ONIOM option in G98 for a system which is neutral, however high layer is negatively charged (-1) while low layer is positively charged (+1) because each of them include different molecules. Is it possible to put these information about charges of each layer in input file? Jolanta Grembecka Institute of Organic Chemistry, Biochemistry and Biotechnology Wroclaw University of Technology From chemistry-request@www.ccl.net Wed Feb 24 11:23:13 1999 Received: from seas.marine.usf.edu (seas.marine.usf.edu [198.116.54.30]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA20213 Wed, 24 Feb 1999 11:23:12 -0500 (EST) Received: from luo.marine.usf.edu (luo.marine.usf.edu [198.116.54.87]) by seas.marine.usf.edu (8.9.1a/8.9.1) with SMTP id LAA27502 for ; Wed, 24 Feb 1999 11:23:08 -0500 (EST) Message-ID: <001f01be6012$26979a20$573674c6@luo.marine.usf.edu> From: "Yu-Ran Luo" To: Subject: RE: CCL: Thermochemistry of radicals Date: Wed, 24 Feb 1999 11:24:26 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3155.0 Hi, Sergio, You wrote: "What is the best method to calculate energies of reactions involving radicals? Is compound methods like CBS-Q as good choice?" I think I could give some answers for your questions. Please show me what reaction(s), free radicals are you interested in. I would point out the values of the BDEs (bond dissociation energies), heats of formation, and more. Yu-Ran Luo, Ph. D. http://molenergetics.simplenet.com From chemistry-request@www.ccl.net Wed Feb 24 11:23:24 1999 Received: from vega.ciam.unibo.it (vega.ciam.unibo.it [137.204.214.165]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA20223 Wed, 24 Feb 1999 11:23:20 -0500 (EST) Received: from gandalf.ciam.unibo.it (localhost [127.0.0.1]) by vega.ciam.unibo.it (8.8.7/8.8.7) with ESMTP id RAA00405 for ; Wed, 24 Feb 1999 17:32:25 +0100 Sender: giampi@vega.ciam.unibo.it Message-ID: <36D42999.F4809D38@gandalf.ciam.unibo.it> Date: Wed, 24 Feb 1999 17:32:25 +0100 From: "G.P. Miscione" X-Mailer: Mozilla 4.07 [en] (X11; I; Linux 2.0.36 i586) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Summary: Molecular mechanics (metals) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, the following was my original question: "could anybody please let me have info/advises on good molecular mechanics software package supporting transition metals?" And below I listed all the answers i've received so far. Thanks to everyone who replied to me: i did appreciate your help. Best regards, G.P. Miscione -- From: Matthew F Schlecht The PC-based modeling program PCMODEL has a good algorithm for calculating the structure of transition metal compounds. More information on it may be found at the Serena Software website at: http://www.serenasoft.com/ -- From: whited@matrix.newpaltz.edu The Universal Force Field produced by MSI in San Diego is a good one. -- From: "Dr. Klaus Stark" with MSI's Discover or the OFF (Open Force Field) force field engine you can work with several force fields and perform energy minimization, molecular dynamics and MD analysis. There are basically two force fields which can handle a great part of the periodic table. These are the so-called rule based force fields which rely on atomic parameters coupled with theoretically and empirically derived rules for generating explicit force field parameters. In Discover the Extensible Systematic Force Field (ESFF) is such a rule-based force field. ESFF was derived using a mixture of DFT calculations on dressed atoms to obtain polarizabilities, gas-phase and crystal structures. The training set included molecules containg each element in the first six periodes (except the inert gases). Parameters and charges are generated on-the-fly, based on the configuration, the local environment and the derived rules. Within OFF you can access the Universal Force Field (UFF) by Rappe and Goddard. Like ESFF it is a rule based force field, the parameters being generated based on physically realistic rules. UFF has full coverage of the periodic table. For more information, please visit our web site at http://www.msi.com --- From: "Andruski, Stephen W." I know that the commercial package Alchemy 2000 from Tripos supports various transition metals. I don't know how good their force field is for these elements, but support is there. Spartan from Wavefunction may also support transition elements since their PM3(tm) semi-empirical method supports them, but I'm not sure about their MM methods. -- From: David Young Molecular mechanics on transition metals is problematic. It turns out not to be as easy to develop a reliable method as is the case for organic simulation by molecular mechanics. In the past, many researchers have parameterized a transition metal for a specific coordination in a specific class of compounds. The force field that is probably best without manual manipulation is UFF. It is designed and sold by MSI. It is also starting to get incorporated into other packages, such as Gaussian 98. Even with this, I would recommend that you test it on a known structure and examine your all of your results carefully. --- From: Eckart Spitzberg I use for my calculations of tungsten-komplexes the program package gaussian94 from gaussian inc. ( http://www.gaussian.com ), and I think, it is very useful. From chemistry-request@www.ccl.net Wed Feb 24 11:29:59 1999 Received: from lovelace.usfca.edu (root@lovelace.usfca.edu [138.202.192.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA20376 Wed, 24 Feb 1999 11:29:58 -0500 (EST) Received: from delta.usfca.edu (deltaenet.usfca.edu [138.202.3.254]) by lovelace.usfca.edu (8.9.1a/8.9.1) with SMTP id IAA04171 for ; Thu, 25 Feb 1999 08:30:55 -0800 Date: Thu, 25 Feb 1999 08:30:55 -0800 Received: from [138.202.97.100] by delta.usfca.edu with ESMTP for chemistry@www.ccl.net; Wed, 24 Feb 1999 8:29:58 -0800 X-Sender: karney@pop.admin.usfca.edu Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CCL From: William Karney Subject: memory usage in G94 Hello, I'm using Gaussian94 on an SGI Octane. We recently upgraded to 768MB of RAM, with the intention of running large jobs (e.g. CASSCF) incore. But for some reason, I'm unable to use any more than about 512MB for a single job. That is, I can specify up to mem=63000000 in the input file, and it will run (though, it seems, more slowly than normal), but if I request more than 63 megawords of memory, the job just hangs up. Does anyone have any suggestions as to how to overcome this problem, and persuade G94 to use more than 63 MW of memory for a job? Any advice would be greatly appreciated. Thanks, William From chemistry-request@www.ccl.net Wed Feb 24 03:09:00 1999 Received: from asterix.uni-muenster.de (chan@ASTERIX.UNI-MUENSTER.DE [128.176.188.90]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA15857 Wed, 24 Feb 1999 03:08:57 -0500 (EST) Received: from localhost (chan@localhost) by asterix.uni-muenster.de (8.8.8/8.7.5) with ESMTP id IAA294190 for ; Wed, 24 Feb 1999 08:08:57 GMT X-Authentication-Warning: asterix.uni-muenster.de: chan owned process doing -bs Date: Wed, 24 Feb 1999 09:08:57 +0100 (MEZ) From: "Jerry C.C. Chan" To: chemistry@www.ccl.net Subject: Summary: AMD-K6/linux for G98 Message-ID: Sorry for any duplication, it seems the following summary didn't get posted at the first time. ------------------------- Many thanks for those who responsed to my post. In short, P-II is highly recommended, DEC Alpha (21164) is a good alternative, Celeron-based machine MAY be a good choice (see both positive and negative comments below), AMD-K6 is not at all useful for numerical calculation. The 11th response from Prof Teppen is very interesting that the performance of his 4-processor-P-II linux box from Peter Pulay's company (cost $11,000) is only 15% slower than a Cray T3E-1200 with 4 processors. Please excuse me for removing some of the signatures in order to shorten this summary. Original post: > We have a plan to get a linux box equipped with AMD-K6 for Gaussian 98 > calculations. However, it seems that the recommended blas library and > Portland Fortran compiler are optimized for Intel CPU only (I may be > mistaken saying so). I would be grateful if anyone could share his/her > experience concerning the following thoughts > i. pay more money to buy Intel processor > ii. go on with our plan (assuming that the performance of Linux/AMDK6-G98 > won't be very different from Linux/IntelPII-G98) > iii. keep the AMD but switch to NT/G98W instead of linux/G98 ++++++Responses++++++ 1. From: Drake Diedrich BLAS isn't apparently heavily used in Gaussian (only in CI methods), but... you may still be better off getting an Intel CPU. On heavy floating point and memory bandwidth I have benchmarked a pentium-166 outperforming an AMD K6/2-300. Pentiums (and later Intel processors) have pipelined floating point units while AMD and Cyrix have only a single floating point execution unit. AMD processors are not competitive with the pentium-II. You should add the DEC Alpha (21164) to your shortlist of alternatives. I haven't benchmarked Gaussian on it, but if you search the web you'll find a hand coded BLAS library for the Alpha that achives 800 MFlops on a 600MHz chip. The ASCI-Red BLAS library gets only 180 MFlops on our Pentium-II/266. -Drake 2. From fparnold@balihai.uchicago.edu Tue Feb 23 10:46:42 1999 If you follow the links through the Beowulf page (www.beowulf.org) to their archive for February of 1999 (or possible Jan) there is a comparison of CHARMm run times on the K6 vs. Celeron. Basically, CHARMm is slow on the K6, but runs on teh Celeron at the same speed of the PII. So, if you're not cache limited, this is a cheap option. IF you are, then the K6 if probably ok. My personal results with GAMESS-US indicates that the K6-233 is slightly faster than a P200 classic, and roughly 5% faster than an SGI O2 with an R5000 processor and secondary cache. Unfortunately, the real answer therefore is, "buy one, and benchmark it yourself". If you get good numbers, buy more and make a cluster out of them. If you don't, you can probably return it and just be out the shipping fee. -fred 3. From pczyryca@smurf.chem.usu.edu Tue Feb 23 10:46:45 1999 K6 is slower than PentiumII (with the same clock). Especially on floating point operations. This is not OS dependent, so I wouldn't expect better performance with NT/G98W combination. Probably it's the best option to spend some more money and buy PentiumII. Regards, * Przemek Czyryca, pczyryca@smurf.chem.usu.edu * 4. From gammadas@telis.org Tue Feb 23 10:46:49 1999 I had the same questions and similar experiences for g94w/g98w as mentioned in the message below---I would pay more and get the Intel PII(PIII will be available in 2 wks!) Also check 2nd message (Jerry: the next message). Hope it helps! 5. From: "Dr.Christian M¸ck-Lichtenfeld" I have a small number of PCs at hand, which are run under Windows NT and Linux. Although the hardware is not exactly the same, one can come to the overall conclusion that the AMD processors are about 1.5 - 2 times slower than the Intel machines. Even a PentiumII with 266 MHz was found to run a moderate G98W-job in about 60% of the time that an AMD K6/2 with 300 MHz needed (both with at least 128MB RAM). A comparison of several Mopac jobs (Mopac93/Linux) on the AMD K6/2 (300MHz) and on a PentiumII (333MHz) gave the same result (t(AMD)/t(PII) = 1.5 ... 2). I am not a hardware expert but I would suppose that the different architecture of the CPUs clearly favours Intel over AMD, due to the better performance in floating point operations. For the aquisition of new machines I therefore would strongly suggest Intel over AMD. I would be very interested to hear from the experiences of other users, so please forward their answers or summarize if possible. Best wishes Christian Mueck-Lichtenfeld 7. From Steven.Creve@dsm-group.com Tue Feb 23 10:46:52 1999 do anything but the last suggestion. WindowsNT is really a *bad* choice for doing (any kind of) calculations. I would suggest you contact the people at Gaussian with this problem. Steven 8. From: val > i. pay more money to buy Intel processor It seems yes, see comments below. > ii. go on with our plan (assuming that the performance of Linux/AMDK6-G98 > won't be very different from Linux/IntelPII-G98) Using GAMESS ab-initio program under Linux we found that Intel PII-350 is significantly faster then AMDK6-350 (in order of 50%) even without any specific blas libraries. If your budget allows, go to the PII CPU. On the other hand, Celeron shows very good performance: Celeron-300A is close to AMDK6-350, Celeron 333 expected to be a little faster. Both are really cheap now. I have a small collection of GAMESS/ab-initio benchmarks under linux on my homepage: http://nmr.ioc.ac.ru/Staff/AnanikovVP/ > iii. keep the AMD but switch to NT/G98W instead of linux/G98 This is very old (and dangerous ;) question, you may look to the CCL archives, the last discussion finished not long ago. For example, a part of the email from Mike Frisch ; CCL Tue, 5 Jan 1999: ".. We use the same compiler (Portand) and blas libraries on both Windows/NT and Linux, and performance is similar. The differences in reported times are a few percent and probably reflect Linux reporting system time overhead (as other unix versions do) while this isn't included on a per-process basis under NT. Elapsed times are sometimes a bit better under Linux because of better I/O, but the best summary of the situation is that there isn't a signficant performance diffence for running a single, stand-alone job under one OS or the other." best regards, Valentin. 9. From ivan@lipid.biocomp.unibo.it Tue Feb 23 10:46:57 1999 > i. pay more money to buy Intel processor That is the way to go. AMD K6 is a great cpu, but NOT for scientific and technical applications. Its Floating-point unit is VERY slow when compared to intel one. Get a real PII, the fastest you can afford, don't buy a Celeron-based machine. BTW i tested both CPU with G94. > ii. go on with our plan (assuming that the performance of Linux/AMDK6-G98 > won't be very different from Linux/IntelPII-G98) Once more, just to stress it.... I don't think the small saving is absolutely worth the the performance penalty that you have with K6 with scientific and technical programs. > iii. keep the AMD but switch to NT/G98W instead of linux/G98 linux is more stable. go for it. -- Dr. Ivan Rossi - CIRB Biocomputing Unit e-mail: ivan@lipid.biocomp.unibo.it WWW: http://www.biocomp.unibo.it/ivan 10. From daniels@kemi.uu.se Tue Feb 23 10:47:00 1999 I haven't tried gaussian on the AMD-k6, but from my experiences I would *not* recommend using the K6 for floating point stuff. I really like the performance of the K6 for regular stuff like editing, compiling, but the fp perfomance is simply not good enough. my experience is that the pii is about 50 % faster than the k6 with the same frequency. the processor is only part of the computer anyway, you still have to pay the same money for case, monitor, disks etc, so if the final computer is perhaps 20 % more expensive with the PII, it is still worth it for fp stuff. What may break down my argument is that in my calculations, the fp is the bottleneck. In your case it may be the disk, so... best regards Daniel Spångberg Inorganic Chemistry Uppsala University Sweden. 11. From teppen@pilot.msu.edu Tue Feb 23 10:47:05 1999 If I may propose a fourth option in addition to the three you posted: Peter Pulay at the University of Arkansas is a true pioneer of quantum chemistry - for example, his contributions were cited in Pople's official Nobel Prize announcement this past fall. He is a former professor of mine and I like him very much, but I have no other interest in promoting his new company. Pulay has been working on optimized quantum codes since the 1960s and he just started a company to sell them this past year. He has 5-6 coworkers including Jon Baker, another master of optimization methods. Several years ago, Pulay began to parallelize his program for cheap PCs running Linux, and they now have a system they can sell. Their company is "Parallel Quantum Solutions" and pulay's e-mail is "pulay@pqs-chem.com". They build their own PCs and sell a software-hardware bundle. I paid $11,000 for a 4-processor (400 MHz Pentium IIs) machine with Linux and the quantum software installed. I have just got the machine, but benchmarks indicate that this machine has exceedingly good performance/price. For pinene using DFT/B3LYP with large basis sets, for example, the machine i bought for $11,000 was faster than a Cray T3E-600 with 4 processors and only 15% slower than a Cray T3E-1200 with 4 processors, both running parallel Gaussian 94. (The G94 calculations were done by Sosa and Frisch, so were probably pretty well optimized for the machine, see last July 15 number of J. Comput. Chem. Sosa et al. Vol 19, p. 1053). I haven't priced those machines but they must be >$100k. If you want to benchmark against one of your own machines, Pulay would be happy to do some calculations for you. Again, I have no financial interest in telling you this, but it seems like a great product for working quantum chemists. The graphical interface is not great, but it is adequate. They put their time into optimizing code. Best wishes, Brian ********************** Dr. Brian J. Teppen Assistant Professor Department of Crop and Soil Sciences Plant and Soil Science Building, Room 538 Michigan State University East Lansing, MI 48824-1325 phone: 517-353-5215 fax: 517-355-0270 e-mail: teppen@pilot.msu.edu 12. From haasj@ubaclu.unibas.ch Tue Feb 23 10:47:08 1999 i am a chemistry student in the very last three weeks of studying. I am using g98 /molden /k6-2-300 and RH 5.2 Linux and 96MB of RAM. I have encountered that the speed is ok, but not as fast compared to a PII. If i might I would recon you to buy the K7 (will probably come out this year) with the EV6 bus protocol of a DEC ALPHA processor 21264. In later times you would have the opportunity to exchange the proc against an 21264 - what ever clockspeed... nice option i think. With a PII you are at the limit of only increasing clockspeed if even possible, although PII are better in floating point operations. DEC Alpha is for sure a good choice for later. K6-3 (sharptooth) is also quite nice proc to think of cheaper than PII but should be equally fast.. (I can only assume that NT system is equally fast)... greetings juergen haas uni basel org. chem dep. feel free to contact me again 13. From eugene.leitl@lrz.uni-muenchen.de Tue Feb 23 10:47:10 1999 AMD K6 ist voll kompatibel zu PPro/P II CPU. Allerdings koennte Celeron das bessere Preis/Leistungsverhaeltnis bieten. Vielleicht auf K6-3 oder sogar K7 warten? MfG, Eugen 14. From RedAndr@anrb.ru Tue Feb 23 10:47:12 1999 It is not good idea buying AMD/K6 CPU for floating point calculations. Intel processors with same price as AMD have more powerful FPU performance. In addition all compilers can do optimization only for Pentium/Pentium Pro unlike AMD or Cyrix. Therefore you have to forget about using AMD in numerical purposes. You can also buy multiprocessor station with Intel processors unlike AMD. About Linux and NT. Our experiments shows that Linux haven't advantage over Windows 95/NT in numerical calculations. Best regards, Andrew mailto:RedAndr@anrb.ru 15. From gaussian.com!fox@lorentzian.com Tue Feb 23 10:47:15 1999 At this point I cannot vouch for proper operation of G98 on an AMD processor. We do not have plans for supporting this as a platform. While most things work on AMD I have at least one site with a problem trying to run G98W and have several sites that have demonstrated problems with Cyrix processors which make it impossible to run G98. In short I recommend you get Intel. Douglas J. Fox Director of Technical Support help@gaussian.com -----end of summary------ From chemistry-request@www.ccl.net Wed Feb 24 12:06:06 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA20763 Wed, 24 Feb 1999 12:06:06 -0500 (EST) Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id MAA17313; Wed, 24 Feb 1999 12:06:05 -0500 (EST) Date: Wed, 24 Feb 1999 12:06:03 -0500 (EST) From: Jan Labanowski To: chemistry@www.ccl.net cc: Jan Labanowski Subject: 2000-2001 Fulbright Scholar Program grants (fwd) Message-ID: ---------- Forwarded message ---------- Date: Tue, 23 Feb 1999 16:05:54 -0500 From: jherninko@iie.org To: CHEMISTRY@iserver.iie.org Subject: 2000-2001 Fulbright Scholar Program grants CIES would like to bring to your attention the start of the 2000-2001 competition for Fulbright awards to faculty and professionals and ask your help in making these opportunities widely known. The competition opens March 1, with an August 1 deadline for Fulbright lecturing and research grants worldwide. Please see the attached announcement. The Fulbright Scholar Program offers opportunities in all disciplines and professional fields. Professionals outside academe participate, as do university faculty and administrators from 4- year colleges and universities, community colleges, and minority-serving institutions. Each year's grantees include not only scholars from academe, but also professionals from the business community, independent scholars, artists, research scientists, applied professionals in technical fields, government employees, journalists, lawyers, and many others. If you think this program would be of interest to your colleagues, please forward the attached announcement. As the competition deadline is August 1, it would need to be sent no later than June/early July. We very much appreciate your assistance. ----------------------------------------------------------------------- 2000-2001 FULBRIGHT AWARDS FOR U.S. FACULTY AND PROFESSIONALS Opportunities for lecturing or advanced research in over 130 countries are available to college and university faculty and professionals outside academe. U.S. citizenship and the Ph.D. or comparable professional qualifications are required. For lecturing awards, university or college teaching experience is expected. Foreign language skills are needed in some countries, but most lecturing assignments are in English. DEADLINES: May 1, 1999, for distinguished Fulbright chairs in Western Europe and Canada August 1, 1999, for lecturing and research grants in academic year 2000 2001 November 1, 1999, for international education and academic administrator seminars January 1, 2000, for NATO advanced research fellowships and institutional grants FOR MORE INFORMATION: USIA Fulbright Scholar Program Council for International Exchange of Scholars 3007 Tilden Street, NW, Suite 5L, Box PLST Washington, DC 20008-3009 Telephone: 202.686.7877 World Wide Web: www.cies.org E-mail: apprequest@cies.iie.org (requests for application materials only) From chemistry-request@www.ccl.net Wed Feb 24 12:55:22 1999 Received: from hermes.aston.ac.uk (hermes.aston.ac.uk [134.151.79.46]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id MAA21448 Wed, 24 Feb 1999 12:55:18 -0500 (EST) Received: from pharm78100.aston.ac.uk [134.151.78.100] by hermes.aston.ac.uk with smtp (Exim 1.82 #3) id 10FiaR-0000Xv-00; Wed, 24 Feb 1999 17:59:07 +0000 Comments: Authenticated sender is From: "chaudash@aston.ac.uk" Organization: aston.ac.uk To: chemistry@www.ccl.net Date: Wed, 24 Feb 1999 17:57:48 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Biological relevance of aluminium Reply-to: chaudash@aston.ac.uk Priority: normal X-mailer: Pegasus Mail for Windows (v2.54) Message-Id: Hello ccl'ers, A while back I wrote asking if anyone knew of any biological role for aluminium. To my knowledge there is no known relevance of this metal in biological sytems. However I did receive a reply, where someone mentioned that aluminium plays a part in alcohol dehydrogenase. I have looked extensively to find out more to no avail. I would be most grateful for any input. Many thanks for your time From chemistry-request@www.ccl.net Wed Feb 24 23:55:22 1999 Received: from mcbsgs1.imcb.nus.edu.sg (mcbsgs1.imcb.nus.edu.sg [137.132.42.51]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id XAA26975 Wed, 24 Feb 1999 23:55:17 -0500 (EST) Received: from imcb.nus.edu.sg ([137.132.42.198]) by mcbsgs1.imcb.nus.edu.sg (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id MAA07684 for ; Thu, 25 Feb 1999 12:59:18 +0800 Message-ID: <36D4D612.D15DB959@imcb.nus.edu.sg> Date: Thu, 25 Feb 1999 12:48:18 +0800 From: mcbskt Reply-To: mcbskt@mcbsgs1.imcb.nus.edu.sg Organization: Institute of Molecular & Cell Biology X-Mailer: Mozilla 4.08 [en] (WinNT; I) MIME-Version: 1.0 To: CCL Subject: Problem installing Naccess v2.1 software for LINUX RedHat Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I tried to install Naccess ( software for calculating solvent accessibility of protein) in a LINUX RedHat 5.1. The following is some information for diagnosis: Anyone with similar problem before and had solved it, please advice. Thank you. Seow, Kah-Tong IMCB, NUS ################################################## The compiler in Linux RedHat is g77 $ naccess installation program $ ---------------------------- $ installing naccess in directory /naccess2.1.1 $ created naccess - cshell script $ compiling accall.f $ done Output of csh install.scr with modification in install.scr to f77 -Wall accall.f: In program `accall': accall.f:71: warning: unused variable `hgen' accall.f:65: warning: unused variable `reslabel' accall.f:62: warning: unused variable `b' accall.f:43: warning: unused variable `outputtype' accall.f:270: warning: `nchain' might be used uninitialized in this function accall.f: In subroutine `solva': accall.f:740: warning: unused variable `c' accall.f: In subroutine `vanin': accall.f:1257: warning: unused variable `ok' accall.f:1255: warning: unused variable `aa4' Screen output of naccess xxx.pdb ******************************** naccess: using vdw.radii in local directory naccess: using STD FILE in local directory startio: error in format apparent state: unit 4 named .log last format: (a,i,a,i,a) lately writing sequential formatted external IO Abort (core dumped) content of xxx.log for the above xxx.pdb ********************************** ACCALL - Accessibility calculations