From ccl@www.ccl.net Mon Aug 4 07:15:27 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id HAA19928; Mon, 4 Aug 1997 07:12:26 -0400 (EDT) Received: from info.cyf-kr.edu.pl for mbskowro@cyf-kr.edu.pl by bedrock.ccl.net (8.8.6/950822.1) id HAA20466; Mon, 4 Aug 1997 07:11:59 -0400 (EDT) Received: from kinga.cyf-kr.edu.pl (kinga.cyf-kr.edu.pl [149.156.4.10]) by info.cyf-kr.edu.pl (8.8.6/8.8.6) with ESMTP id NAA10095 for ; Mon, 4 Aug 1997 13:11:51 +0200 (METDST) Received: (from mbskowro@localhost) by kinga.cyf-kr.edu.pl (8.8.6/8.8.6) id NAA26641 for chemistry@ccl.net; Mon, 4 Aug 1997 13:07:36 +0200 (METDST) From: Marek Skowronek Message-Id: <199708041107.NAA26641@kinga.cyf-kr.edu.pl> Subject: Oxford&Cambridge Data Base To: chemistry@ccl.net Date: Mon, 4 Aug 1997 13:07:36 +0200 (METDST) X-Mailer: ELM [version 2.4ME+ PL32 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear Netters, I should be very grateful if send me some information (www page or something like that) about CAMBRIDGE CRYSTALOGRAPHIC DATA CENTRE , OXFORD DATABASE, or related databases. Thank you in advance Marek Skowronek From shokhen@post.tau.ac.il Mon Aug 4 08:15:28 1997 Received: from post.tau.ac.il for shokhen@post.tau.ac.il by www.ccl.net (8.8.3/950822.1) id HAA19952; Mon, 4 Aug 1997 07:28:36 -0400 (EDT) Received: from etgar.tau.ac.il (etgar.tau.ac.il [132.66.16.7]) by post.tau.ac.il (8.8.5/8.8.4) with ESMTP id OAA20766 for ; Mon, 4 Aug 1997 14:28:34 +0300 (IDT) Received: from localhost (shokhen@localhost) by etgar.tau.ac.il (8.8.5/8.7.3) with SMTP id OAA07108 for ; Mon, 4 Aug 1997 14:28:24 +0300 (IDT) X-Authentication-Warning: etgar.tau.ac.il: shokhen owned process doing -bs Date: Mon, 4 Aug 1997 14:28:24 +0300 (IDT) From: shochen michael To: chemistry@www.ccl.net Subject: Reliability of the solvation models in GAUSSIAN Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters In my current work I need to estimate oxidation potentials for sevelal molecules. In other words, I need to calculate the energy difference between ground state and cation-radical (lowest doublet). I have experimental estimations of the oxidation potentials for some of my compounds in water solution. All of my molecules contain three sulfonic groups (SO3-), which of course are ionized in water. Thus, I have as a ground state anionic species with the charge -3, which do not exist in vacuum as systems with negative orbital enrgies of their HOMO (the oxidized form has the charge -2). Vacuum calculations are irrelevant to my compounds, so I have used a reaction field model implemented in GAUSSIAN-94 to simulate water solution. I have used IPCM model with dielectric constant 80. The level of quantum calculations was B3LYP/6-31G* (my molecules are very big, so I can't use more extensive basis set with diffuse functions). Unfortunately, for several cases I got very big (more than 1 eV) difference between the calculated in my model and experimental values of the oxidation potentials. My question is: How really are reliable the estimations of the solvation effects in the IPCM model? Do somebody know references on examples providing the comparison between theoretical and experimantal estimations of solvation energies, or any physical values, which are dependent on the solvation effects for the IPCM model ? Thank you in advance. Michael ********************************************************* Dr. Michael Shokhen Senior researcher, Department of Biochemistry, G.S.Wise Faculty of Life Sciences, Tel-Aviv University, 69978, Tel-Aviv, Israel. Fax: 972-3-6415053 Email: shokhen@etgar.tau.ac.il ********************************************************* From cdac.ernet.in!gadre@parcom.ernet.in Mon Aug 4 10:15:27 1997 Received: from sangam.ncst.ernet.in for cdac.ernet.in!gadre@parcom.ernet.in by www.ccl.net (8.8.3/950822.1) id JAA20527; Mon, 4 Aug 1997 09:54:26 -0400 (EDT) Received: from iucaa (iucaa.ernet.in [144.16.31.4]) by sangam.ncst.ernet.in (8.7.5) with SMTP id TAA08635 for ; Mon, 4 Aug 1997 19:30:15 +0530 (GMT+05:30) Received: from iucaa.iucaa.ernet.in by iucaa (5.65v3.2/SMI-4.1) id AA12011; Mon, 4 Aug 1997 19:18:16 +0500 Received: by parcom.cdac.ernet.in (4.1/SMI-4.1) id AA16480; Mon Aug 4 18:46:52 1997 (GMT + 0530) Date: Mon Aug 4 18:46:52 1997 (GMT + 0530) From: gadre@cdac.ernet.in Message-Id: <9708041316.AA16480@parcom.cdac.ernet.in> To: CHEMISTRY@www.ccl.net Subject: Basis sets for cations Dear Sirs : Could someone provide me with the all electron 6-31G** basis sets for the following cations? Ca2+, K+, Na+, Mn2+, Fe2+ and Zn2+. Thanks in advance. Shridhar Gadre e-mail : gadre@parcom.ernet.in From ccl@www.ccl.net Mon Aug 4 10:21:49 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id JAA20430; Mon, 4 Aug 1997 09:41:08 -0400 (EDT) Received: from theory.tc.cornell.edu for cal@tc.cornell.edu by bedrock.ccl.net (8.8.6/950822.1) id JAA23940; Mon, 4 Aug 1997 09:41:05 -0400 (EDT) Received: from [128.84.181.30] (PANTHER.TC.CORNELL.EDU [128.84.181.30]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with SMTP id JAA31657; Mon, 4 Aug 1997 09:40:54 -0400 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 4 Aug 1997 09:40:58 -0400 To: chemistry@ccl.net From: cal@TC.Cornell.EDU (Linda Callahan) Subject: Symposium Announcement Cc: cal@TC.Cornell.EDU Structural Biology Symposium The Cornell Theory Center (CTC) announces its fifth annual symposium for biomedical scientists. This year's symposium, to be held October 7 and 8 on the Cornell University campus, will highlight research being done in the field of structural biology. The symposium is funded by the National Center for Research Resources at the National Institutes of Health as part of CTC's Parallel Processing Resource for Biomedical Scientists. Among the speakers: Paul Beroza, Scripps Research Institute William Eaton, NIH Robert Jernigan, NIH Andrej Kolinski, Scripps Research Institute Thanasis Panogiotopoulos, Cornell Andrej Sali, Rockefeller Peter Wolynes, University of Illinois Michael Zerner, University of Florida Additional information and registration form can be found at http://www.tc.cornell.edu/Events/Structural.Biology.97/index.html or contact Donna Smith - donna@tc.cornell.edu From mn1@helix.nih.gov Mon Aug 4 11:27:13 1997 Received: from helix.nih.gov for mn1@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id KAA20886; Mon, 4 Aug 1997 10:47:27 -0400 (EDT) Received: (from mn1@localhost) by helix.nih.gov (8.8.5/8.8.5) id KAA15603 for CHEMISTRY@www.ccl.net; Mon, 4 Aug 1997 10:47:29 -0400 (EDT) Date: Mon, 4 Aug 1997 10:47:29 -0400 (EDT) From: "M. Nicklaus" Message-Id: <199708041447.KAA15603@helix.nih.gov> To: CHEMISTRY@www.ccl.net Subject: Re: Alpha + Linux ? On Fri, 1 Aug 1997, Cheol Choi wrote: > According to the SPEC benchmark, Dec Alpha seems to be the > fastest processor currently. > And I know some companies are selling Alpha workstations with Linux OS at > very reasonable price. > Is there anyone who has good experience with Alpha + Linux combination? We've had some experience with Alpha + Linux recently, and are going to have more very soon. Has it been good? Yes and no. The Alpha chip is indeed a very fast processor. The new motherboards with the DEC Pyxis chip set promise to be even faster, 600 MHz systems are selling (albeit still quite expensive), and processors with clock rates of 800 MHz and higher are in the pipeline. What's the drawback then? Mostly the software. The Linux for the Alpha (axp-linux) is much less mature and stable than Linux for the x86 type processors. A big problem are the compilers. f2c is plain buggy, and gcc and the linker also have their problems. If you want to know more (probably more than you want to know...) about these technical axp-linux issues, you can follow the discussion on the mailing list axp-list@redhat.com (to subscribe: send e-mail to axp-list-request@redhat.com with 'subscribe' as the subject), or check the newsgroup comp.os.linux.alpha. The software we tested on axp-linux was: CHARMM runs GAMESS runs AMSOL runs Gaussian 94 doesn't compile (see also previous postings on the CCL) When I last checked some of the Web sites on scientific applications for Linux, such as http://SAL.kachinatech.com/Z/2 or http://chpc06.ch.unito.it/chem_linux.html, I counted more than 70 Chemistry/Biology related programs. We sure haven't tested them all, but I'd guess if you get the source code for them, you could give it a shot at compiling them on an Alpha Linux system. If you have access to a Digital Unix system, you can actually compile your program on the DEC system and then run it on the Alpha Linux machine -- the executables are binary compatible (if you use static linking for the libraries). This doesn't always work (didn't work for G94), but we've used this method repeatedly for other programs. The benchmarks we ran showed very nice results indeed. The speedup we saw for various application relative to a Pentium PRO 200 MHz system running under Linux was between 1.5 and 2.2. From the clock rates, you would expect 2.5 (we used a 500 MHz Alpha chip). The advanced chip architecture itself might allow even higher numbers. The reason we havent't seen those numbers (yet) are most likely compiler issues. I can only recommend that you test various compiler options (optimization etc.) if not different compiler to see which gives you the fastest code. The bottom line, from my point of view, is: It's a great platform, but still in its early stages. So, if you like to patch operating system source code, rebuild the kernel, tweak the compilers, and do other system 'hacking' regularly, go for it (...it's not really that bad, but you get my drift). We *are* using such a system to do real comp.chem. work. However, if you want a system that is totally out-of-the-box, runs every known application without a problem, has plenty of stable compilers, etc., then you'd probably want to wait a little bit longer. Marc ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 37, Rm 5B29 Phone: (301) 402-3111 BETHESDA, MD 20892-4255 USA Fax: (301) 496-5839 http://www.nci.nih.gov/intra/lmch/MCNBIO.HTM Laboratory of Medicinal Chemistry, National Cancer Institute, & Lab. of Structural Biology, Div. of Computer Research and Technology ------------------------------------------------------------------------ From peter@cherwell.com Mon Aug 4 12:31:43 1997 Received: from cherwell.com for peter@cherwell.com by www.ccl.net (8.8.3/950822.1) id MAA21580; Mon, 4 Aug 1997 12:10:16 -0400 (EDT) Received: from mersey.cherwell.com by cherwell.com (4.1/SMI-4.1) id AA28892; Mon, 4 Aug 97 17:10:19 BST Message-Id: <3.0.1.32.19970804170807.00815100@cherwell.com> X-Sender: peter@cherwell.com X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Mon, 04 Aug 1997 17:08:07 +0100 To: chemistry@www.ccl.net From: Peter Tebbutt Subject: ChemSymphony version 2.1 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" ChemSymphony version 2.1 Cherwell Scientific Publishing are pleased to announce the release of ChemSymphony version 2.1. This version presents several improvements and modifications on version 2. Improved rendering and perspective Quicker rendering Improved animation The ability to render proteins as ribbons/strands etc. The use of filters to automatically recognise common file formats More fromats used including Gaussian and MOPAC Z-matrix. New graphic interaface for several applets ChemSymphony may be viewed and assessed at our web site at: http://www.chemsymphony.com. These pages include extensive examples, tutorials, ordering and new price information. Peter Tebbutt ----------------------------------------------------------- Peter Tebbutt | e-mail: peter@cherwell.com Development Support | Tel: +44 (0)1865 784812 Cherwell Scientific Publishing| Fax: +44(0)1865 784801 Oxford OX4 4GA, UK | http://www.cherwell.com ----------------------------------------------------------- Check Out ChemSymphony - rated top 1% Java applet by JARS http://www.cherwell.com/chemsymphony ----------------------------------------------------------- From brunob@helix.nih.gov Mon Aug 4 14:15:29 1997 Received: from mgcct6.nci.nih.gov for brunob@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id NAA22078; Mon, 4 Aug 1997 13:31:21 -0400 (EDT) Received: from mgcct6 (localhost [127.0.0.1]) by mgcct6.nci.nih.gov (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id OAA08176 for ; Mon, 4 Aug 1997 14:18:23 -0400 Sender: brunob@helix.nih.gov Message-ID: <33E61CEF.2781@helix.nih.gov> Date: Mon, 04 Aug 1997 14:18:23 -0400 From: Bruno Bienfait Organization: National Cancer Institute X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: Computer Chemistry List Subject: G:Alpha + Linux ? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit On Fri, 1 Aug 1997, Cheol Choi wrote: > According to the SPEC benchmark, Dec Alpha seems to be the > fastest processor currently. > And I know some companies are selling Alpha workstations with Linux OS at > very reasonable price. > Is there anyone who has good experience with Alpha + Linux combination? We've had some experience with Alpha + Linux recently, and are going to have more very soon. Has it been good? Yes and no. The Alpha chip is indeed a very fast processor. The new motherboards with the DEC Pyxis chip set promise to be even faster, 600 MHz systems are selling (albeit still quite expensive), and processors with clock rates of 800 MHz and higher are in the pipeline. What's the drawback then? Mostly the software. The Linux for the Alpha (axp-linux) is much less mature and stable than Linux for the x86 type processors. A big problem are the compilers. f2c is plain buggy, and gcc and the linker also have their problems. If you want to know more (probably more than you want to know...) about these technical axp-linux issues, you can follow the discussion on the mailing list axp-list@redhat.com (to subscribe: send e-mail to axp-list-request@redhat.com with 'subscribe' as the subject), or check the newsgroup comp.os.linux.alpha. The software we tested on axp-linux was: CHARMM runs GAMESS runs AMSOL runs Gaussian 94 doesn't compile (see also previous postings on the CCL) When I last checked some of the Web sites on scientific applications for Linux, such as http://SAL.kachinatech.com/Z/2 or http://chpc06.ch.unito.it/chem_linux.html, I counted more than 70 Chemistry/Biology related programs. We sure haven't tested them all, but I'd guess if you get the source code for them, you could give it a shot at compiling them on an Alpha Linux system. If you have access to a Digital Unix system, you can actually compile your program on the DEC system and then run it on the Alpha Linux machine -- the executables are binary compatible (if you use static linking for the libraries). This doesn't always work (didn't work for G94), but we've used this method repeatedly for other programs. The benchmarks we ran showed very nice results indeed. The speedup we saw for various application relative to a Pentium PRO 200 MHz system running under Linux was between 1.5 and 2.2. From the clock rates, you would expect 2.5 (we used a 500 MHz Alpha chip). The advanced chip architecture itself might allow even higher numbers. The reason we havent't seen those numbers (yet) are most likely compiler issues. I can only recommend that you test various compiler options (optimization etc.) if not different compiler to see which gives you the fastest code. The bottom line, from my point of view, is: It's a great platform, but still in its early stages. So, if you like to patch operating system source code, rebuild the kernel, tweak the compilers, and do other system 'hacking' regularly, go for it (...it's not really that bad, but you get my drift). We *are* using such a system to do real comp.chem. work. However, if you want a system that is totally out-of-the-box, runs every known application without a problem, has plenty of stable compilers, etc., then you'd probably want to wait a little bit longer. [ I asked a colleague here in the Lab to help me out and post this for me because this message ended up in CCL's "rejected" file thrice. I'm seeing in this file numerous other messages that don't seem to contain anything offensive or against CCL rules. Maybe Jan could comment on that. ] Marc ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 37, Rm 5B29 Phone: (301) 402-3111 BETHESDA, MD 20892-4255 USA Fax: (301) 496-5839 http://www.nci.nih.gov/intra/lmch/MCNBIO.HTM Laboratory of Medicinal Chemistry, National Cancer Institute, & Lab. of Structural Biology, Div. of Computer Research and Technology ------------------------------------------------------------------------ From mn1@helix.nih.gov Mon Aug 4 18:15:32 1997 Received: from helix.nih.gov for mn1@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id RAA22982; Mon, 4 Aug 1997 17:25:59 -0400 (EDT) Received: (from mn1@localhost) by helix.nih.gov (8.8.5/8.8.5) id RAA01011; Mon, 4 Aug 1997 17:25:56 -0400 (EDT) Date: Mon, 4 Aug 1997 17:25:56 -0400 (EDT) From: "M. Nicklaus" Message-Id: <199708042125.RAA01011@helix.nih.gov> To: CHEMISTRY@www.ccl.net Subject: Alpha + Linux ? Cc: mn1@helix.nih.gov On Fri, 1 Aug 1997, Cheol Choi wrote: > According to the SPEC benchmark, Dec Alpha seems to be the > fastest processor currently. > And I know some companies are selling Alpha workstations with Linux OS at > very reasonable price. > Is there anyone who has good experience with Alpha + Linux combination? We've had some experience with Alpha + Linux recently, and are going to have more very soon. Has it been good? Yes and no. The Alpha chip is indeed a very fast processor. The new motherboards with the DEC Pyxis chip set promise to be even faster, 600 MHz systems are selling (albeit still quite expensive), and processors with clock rates of 800 MHz and higher are in the pipeline. What's the drawback then? Mostly the software. The Linux for the Alpha (axp-linux) is much less matuer and stable than Linux for the x86 type processors. A big problem are the compilers. f2c is plain buggy, and gcc and the linker also have their problems. If you want to know more (probably more than you want to know...) about these technical axp-linux issues, you can follow the discussion on the mailing list axp-list@redhat.com (to subscribe: send e-mail to axp-list-request@redhat.com with 'subscribe' as the subject), or check the newsgroup comp.os.linux.alpha. The software we tested on axp-linux was: CHARMM runs GAMESS runs AMSOL runs Gaussian 94 doesn't compile (see also previous postings on the CCL) When I last checked some of the Web sites on scientific applications for Linux, such as http://SAL.kachinatech.com/Z/2 or http://chpc06.ch.unito.it/chem_linux.html, I counted more than 70 Chemistry/Biology related programs. We sure haven't tested them all, but I'd guess if you get the source code for them, you could give it a shot at compiling them on an Alpha Linux system. If you have access to a Digital Unix system, you can actually compile your program on the DEC system and then run it on the Alpha Linux machine -- the executables are binary compatible (if you use static linking for the libraries). This doesn't always work (didn't work for G94), but we've used this method repeatedly for other programs. The benchmarks we ran showed very nice results indeed. The speedup we saw for various application relative to a Pentium PRO 200 MHz system running under Linux was between 1.5 and 2.2. From the clock rates, you would expect 2.5 (we used a 500 MHz Alpha chip). The advanced chip architecture itself might allow even higher numbers. The reason we havent't seen those numbers (yet) are most likely compiler issues. I can only recommend that you test various compiler options (optimization etc.) if not different compilers to see which gives you the fastest code. The bottom line, from my point of view, is: It's a great platform, but still in its early stages. So, if you like to patch operating system source code, rebuild the kernel, tweak the compilers, and do other system 'hacking' regularly, go for it (...it's not really that bad, but you get my drift). We *are* using such a system to do real comp.chem. work. However, if you want a system that is totally out-of-the-box, runs every known application without a problem, has plenty of stable compilers, etc., then you'd probably want to wait a little bit longer. Marc ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 37, Rm 5B29 Phone: (301) 402-3111 BETHESDA, MD 20892-4255 USA Fax: (301) 496-5839 http://www.nci.nih.gov/intra/lmch/MCNBIO.HTM Laboratory of Medicinal Chemistry, National Cancer Institute, & Lab. of Structural Biology, Div. of Computer Research and Technology ------------------------------------------------------------------------