From Patrick.Bultinck@rug.ac.be Mon Mar 28 02:01:30 1994 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.4/930601.1506) id BAA26002; Mon, 28 Mar 1994 01:46:04 -0500 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA12820 (5.65c/IDA-1.4.4 for ); Mon, 28 Mar 1994 08:45:36 +0200 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA09101; Mon, 28 Mar 94 08:42:53 +0200 Date: Mon, 28 Mar 1994 08:42:52 +0200 (MET DST) From: Patrick Bultinck Subject: Textbook on computational chemistry techniques To: chemistry@ccl.net In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 954 Dear Netters, 1) We do not have a good textbook that provides us with helpful information on the way SCF calculations and such are translated in computer and program lingo. I would like to receive some references to textbooks in which is explained which alogoritms ans such are used in most programs, so I can more or less follow how some programs really work, instead of considering them as black boxes! If I get enough answers I will post a small summary of references to the CCL, since I have not yet seen a lot of questions that refer to this kind of book. 2) Does anybody have knowledge of a Hartree-Fock program written in C (I am not willing to start another "religious discussion" between the C and the Fortran people). Thanks for your time, Patrick Bultinck University of Ghent Krijgslaan 281 (S3) 9000 Gent Belgium Tel. /32/9/264.44.44 Fax. /32/9/264.49.83 E-mail : Patrick.Bultinck@rug.ac.be From braendle@solar.iac.unibe.ch Mon Mar 28 06:01:33 1994 Received: from chx400.switch.ch for braendle@solar.iac.unibe.ch by www.ccl.net (8.6.4/930601.1506) id FAA27551; Mon, 28 Mar 1994 05:24:46 -0500 Received: from arwen.unibe.ch by chx400.switch.ch with SMTP (PP); Mon, 28 Mar 1994 12:24:32 +0200 From: braendle@solar.iac.unibe.ch (Martin Braendle) Message-Id: <9403281024.AA17101@solar.iac.unibe.ch> Subject: QSAR, transition metals, solid state? To: chemistry@ccl.net Date: Mon, 28 Mar 1994 12:24:26 +0200 (DFT) X-Mailer: ELM [version 2.4 PL20] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 8bit Content-Length: 587 Question from a newcomer: Have QSAR methods been applied to transition metal and solid state compounds, and have they been successful? Any pointers to literature are welcome. Thank you. Martin Braendle -------------------------------------------------------------------------------- Martin Braendle, Institute for Inorganic and Physical Chemistry, University of Berne, Freiestr. 3, CH-3012 Berne, Tel. xx41 31 631 42 25, Fax xx41 631 39 94, Email braendle@solar.iac.unibe.ch (or braendle@iac.unibe.ch) -------------------------------------------------------------------------------- From mei@atlas.rc.m-kasei.co.jp Mon Mar 28 07:01:34 1994 Received: from relay2.UU.NET for mei@atlas.rc.m-kasei.co.jp by www.ccl.net (8.6.4/930601.1506) id GAA27710; Mon, 28 Mar 1994 06:29:18 -0500 Received: from uucp1.uu.net by relay2.UU.NET with SMTP (5.61/UUNET-internet-primary) id AAwjeb02986; Mon, 28 Mar 94 06:29:16 -0500 Received: from kddlab.UUCP by uucp1.uu.net with UUCP/RMAIL ; Mon, 28 Mar 1994 06:29:17 -0500 Received: from kddfuji by kddlab.kddlabs.co.jp (5.61/6.2Junet) id AA03514; Mon, 28 Mar 94 20:24:00 +0900 Received: from kogwy.cc.keio.ac.jp by kddfuji.kddlabs.co.jp (5.67+1.6W/KDD-1.02MX) id AA23441; Mon, 28 Mar 94 20:22:25 JST Received: by kogwy.cc.keio.ac.jp (5.67+1.6W+comp-patch/2.8Wb) id AA15365; Mon, 28 Mar 94 20:22:23 JST Received: from atlas.rc.m-kasei.co.jp by mkcgwy.rc.m-kasei.co.jp (4.1/6.4J.6) id AA19090; Mon, 28 Mar 94 19:46:42 JST Received: by atlas.rc.m-kasei.co.jp (4.1/6.4J.6) id AA16891; Mon, 28 Mar 94 19:46:43 JST From: mei@atlas.rc.m-kasei.co.jp (Akinori MURAKAMI) Message-Id: <9403281046.AA16891@atlas.rc.m-kasei.co.jp> To: DSMITH@uoft02.utoledo.edu Cc: chemistry@ccl.net, mei@atlas.rc.m-kasei.co.jp Subject: Re: CCL:energy partitioning question In-Reply-To: Your message of "Wed, 23 Mar 94 12:21:48 EST." <01HAB7TSNOAA00018K@UOFT02.UTOLEDO.EDU> Date: Mon, 28 Mar 94 19:46:43 +0900 The original paper by Kazuo Kitaura and Morokuma is ^^^^^^^^^^^^^ Int. J. Quant. Chem. vol. x, p 325-340 (1976) ' A New Energy Decomposition Scheme for Molecular Interactions within Hartree-Fock Approximation' Usualy called Morokuma's energy partitiong, but seldom Kitaura and Morokuma's. >> Can someone provide me with the references to the original paper(s) by >> Morokuma which describe how to partition energy into its component terms, >> such as dispersion, electrostatic, etc.? Also, if anyone is aware of this >> method being applied to hydrogen bonds or hydrogen bonding systems, please >> forward those references as well. I would appreciate it. >> >> Doug >> >> Douglas A. Smith >> Assistant Professor, Department of Chemistry >> Center for Drug Design and Development >> and >> Chairman-elect, ACS Division of Computers in Chemistry >> >> The University of Toledo >> Toledo, OH 43606-3390 >> >> voice 419-537-2116 >> fax 419-537-4033 >> email dsmith@uoft02.utoledo.edu >> ................................... !!! Note !!! Akinori MURAKAMI My user-ID is not murakami Mitsubishi Kasei Corporation There are more than two murakami Computational Science Laboratory Research Center, Yokohama, JAPAN e-mail mei@m-kasei.co.jp Tel +81(45)-963-3269 Fax +81(45)-963-3982 ................................... From Don_Gregory@MSI.COM Mon Mar 28 10:01:38 1994 Received: from schizoid.msi.com for Don_Gregory@MSI.COM by www.ccl.net (8.6.4/930601.1506) id JAA28516; Mon, 28 Mar 1994 09:04:47 -0500 Received: from msi.com (qmail-gw.msi.com) by schizoid.msi.com (4.1/SMI-4.1) id AA09785; Mon, 28 Mar 94 09:04:15 EST Message-Id: <9403281404.AA09785@schizoid.msi.com> Date: 28 Mar 1994 09:04:11 +0000 From: "Don Gregory" Subject: CHARMm & CHARMM To: "OSC" Cc: Steve_Herbert@MSI.COM Subject: Time:8:50 AM OFFICE MEMO CHARMm & CHARMM Date:3/28/94 On March 27, Ilya Logunov (U.of Illinois) wrote asking about the latest version of CHARMm. First the answer to her question, and then a brief point of clarification. CHARMm is a product available from Molecular Simulations, Burlington, Mass. Western U.S. academic users can call Adam Bernstein at (617) 229-9800 for pricing and information. The standard discount to academics is 90% off commercial list-price. Just to make sure everyone is clear on the difference, CHARMm (little m) is the commercial version, sold by MSI. CHARMM is the academic version distributed by Prof. Karplus' group at Harvard. The added capabilities to CHARMm that make it advantageous are: larger parameter arrays, allowing a wider range of molecular types that can be studied, "graphical" hooks into Quanta which is available *only* from MSI homogeneous or heterogenous clustering (distributed processing) and 12hr/day toll-free customer hot-line support. Just wanted to make sure that academics knew their options, while trying not to sound too much like a sales pitch. My apologies if I failed in the latter. Don Gregory Manager, Application Science, MSI From jkl@ccl.net Mon Mar 28 11:01:37 1994 Received: from krakow.ccl.net for jkl@ccl.net by www.ccl.net (8.6.4/930601.1506) id KAA29129; Mon, 28 Mar 1994 10:03:30 -0500 From: Jan Labanowski Received: from localhost for jkl@ccl.net by krakow.ccl.net (8.6.4/920428.1525) id KAA04139; Mon, 28 Mar 1994 10:03:29 -0500 Date: Mon, 28 Mar 1994 10:03:29 -0500 Message-Id: <199403281503.KAA04139@krakow.ccl.net> To: chemistry@ccl.net Subject: IBM-PC software in CCL archives Cc: jkl@ccl.net Thanks to J. Eric Slone (eslone@mason1.gmu.edu) we have some nice additions to our software directory in CCL archives. Thank you Eric for your work and willingness to share it with us. These are programs for IBM-PC hich he gathered from different archives in the Cyberspace. Some of them are his own. To find out more what is in the software directory send a following message: select chemistry cd software dir quit to MAILSERV@ccl.net. You can get to these files via anonymous ftp, gopher www, and e-mail. To find how to find more, retrieve a help file for the list by sending: help chemistry to MAILSERV@ccl.net Jan jkl@ccl.net From SBOESCH@aardvark.ucs.uoknor.edu Mon Mar 28 13:05:34 1994 Received: from aardvark.ucs.uoknor.edu for SBOESCH@aardvark.ucs.uoknor.edu by www.ccl.net (8.6.4/930601.1506) id MAA02028; Mon, 28 Mar 1994 12:36:28 -0500 From: Message-Id: <199403281736.MAA02028@www.ccl.net> Date: Mon, 28 Mar 94 11:36 CST Subject: Polarizability derivatives from G92 To: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" Dear Netters, Does anyone know if it is possible to get polarizability deriviatives (Raman Intensities) from Gaussian 92 using density functional methods. We think we cannot get the intensities, but if anyone knows for a fact, your response would be appreciated. Thank you very much. Send reply to SBOESCH@aardvark.ucs.uoknor.edu Scott Boesch Department of Chemistry & Biochemistry University of Oklahoma From JeanLuc.Verschelde@rug.ac.be Mon Mar 28 14:03:30 1994 Received: from mserv.rug.ac.be for JeanLuc.Verschelde@rug.ac.be by www.ccl.net (8.6.4/930601.1506) id NAA03634; Mon, 28 Mar 1994 13:24:47 -0500 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AB15833 (5.65c/IDA-1.4.4 for ); Mon, 7 Mar 1994 08:39:01 +0100 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA26155; Mon, 7 Mar 94 08:36:22 +0100 Date: Mon, 7 Mar 1994 08:36:21 +0100 (MET) From: Jean-Luc Verschelde Subject: AB-AG affinities To: OHIO SUPER Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 654 Hi all, Does anybody know a database of antigen-antibody structures with known epitope stuctures ( WT and mutants) and their affinities. I would really appreciate any help. Greetings, Jean-Luc =================================================================================== Verschelde Jean-Luc Lab. for Mathematical Physics Lab. for Biochemistry Krijgslaan 286 S9 9000 Ghent Belgium. Tel.:09/264 47 94 Fax:09/264 49 89 Email:Jeanluc.Verschelde@rug.ac.be =================================================================================== From nauss@ucmod2.che.uc.EDU Mon Mar 28 15:06:57 1994 Received: from ROCK.SAN.UC.EDU for nauss@ucmod2.che.uc.EDU by www.ccl.net (8.6.4/930601.1506) id OAA04688; Mon, 28 Mar 1994 14:20:08 -0500 Received: from ucmod2.che.uc.edu by UCBEH.SAN.UC.EDU (PMDF V4.3-7 #4918) id <01HAIBALRPK08WWH4J@UCBEH.SAN.UC.EDU>; Mon, 28 Mar 1994 14:14:39 EST Received: by ucmod2.che.uc.edu (920330.SGI/920502.SGI.AUTO) for @uc.edu:CHEMISTRY@ccl.net id AA00489; Mon, 28 Mar 94 14:28:52 -0500 Date: Mon, 28 Mar 1994 14:28:52 -0500 From: nauss@ucmod2.che.uc.EDU (Jeffrey L. Nauss) Subject: AM1 vs PM3 To: CHEMISTRY@ccl.net Message-id: <9403281928.AA00489@ucmod2.che.uc.edu> Content-transfer-encoding: 7BIT One of our graduate students asked me the following question. Not being an ab initio expert (or novice or anything) I thought I would pass the question on to the net. What are the differences between AM1 and PM3? How do the algorithms differ? Any noticable differences in calculations? Any pros or cons about the two programs you would care to share? If there is interest, I can summarize for the net. Thank you for your time. Jeff Nauss **************************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: nauss@ucmod2.che.uc.edu * * CCCCCCC Jeffrey.Nauss@UC.Edu * **************************************************************************** From carlos@pap.chem.uic.edu Mon Mar 28 20:01:58 1994 Received: from slipknot for carlos@pap.chem.uic.edu by www.ccl.net (8.6.4/930601.1506) id TAA08992; Mon, 28 Mar 1994 19:30:49 -0500 Received: from pap.chem.uic.edu by slipknot (AIX 3.2/UCB 5.64/4.03) id AA31320; Mon, 28 Mar 1994 18:25:28 -0600 Received: by pap.chem.uic.edu (3.2/SMI-3.0DEV3) id AA20430; Mon, 28 Mar 94 18:36:22 CST Date: Mon, 28 Mar 94 18:36:22 CST From: Carlos Simmerling Message-Id: <9403290036.AA20430@pap.chem.uic.edu> To: CHEMISTRY@ccl.net Subject: MOIL-View user list Dear CCLers, I am in the process of compiling a list of those who are using the program MOIL-View. This will make it easier for me to notify users directly of updates and fixes. IF you are interested in receiving such information, please email me _directly_ at carlos@pap.chem.uic.edu. For those interested in obtaining the program for SGI or IBM RS/6000, source code for version 7.4 is available through anonymous ftp to 128.248.186.70. Carlos Simmerling carlos@pap.chem.uic.edu University of Illinois at Chicago Department of Chemistry