From theochem@ctc.com Tue Sep 19 10:02:48 1995 Received: from server1.ctc.com for theochem@ctc.com by www.ccl.net (8.6.10/950822.1) id KAA07671; Tue, 19 Sep 1995 10:00:26 -0400 Received: by server1.ctc.com (5.65/DEC-Ultrix/4.3) id AA18248; Tue, 19 Sep 1995 10:01:15 -0400 Received: by pauling.ctc.com (940816.SGI.8.6.9/930416.SGI.AUTO) for chemistry@www.ccl.net id JAA21153; Tue, 19 Sep 1995 09:57:41 -0400 From: theochem@ctc.com (Douglas Smith) Message-Id: <199509191357.JAA21153@pauling.ctc.com> Subject: what would be an appropriate journal? To: chemistry@www.ccl.net (Computational Chemistry List) Date: Tue, 19 Sep 1995 09:57:40 -0500 (EDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 546 Please allow me to tap the collective wisdom of the group: Other than the Journal of Chemical Education, what is a good and/or proper journal for the publication of pedagogical articles directed towards undergraduates? The topic is physical/phycial organic/computational chemistry. Doug -- Douglas A. Smith, Ph.D. Principal Technical Staff/Manager Concurrent Technologies Corporation 1450 Scalp Avenue Johnstown, PA 15904 voice: (814) 269-2545 fax: (814) 269-2798 email: theochem@ctc.com Disclaimer: Whatever I say is my own fault. From sanja@indigo.irb.hr Tue Sep 19 11:17:48 1995 Received: from indigo.irb.hr for sanja@indigo.irb.hr by www.ccl.net (8.6.10/950822.1) id LAA10379; Tue, 19 Sep 1995 11:09:27 -0400 Received: by indigo.irb.hr (940816.SGI.8.6.9/930416.SGI.AUTO) for CHEMISTRY@www.ccl.net id QAA12166; Tue, 19 Sep 1995 16:52:51 -0700 From: "sanja" Message-Id: <9509191652.ZM12164@indigo.irb.hr> Date: Tue, 19 Sep 1995 16:52:40 -0700 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@www.ccl.net Subject: polarizability Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear netters, Does any of you know the reference about self atom polarizabilities and anysotropy of the molecular polarizability? I am interested in how I can calculate these parameters from the semiempirical (e.g. AM1) wave function. Sincerely, Zeljka Medven Rugjer Boskovic Institute Zagreb, Croatia e-mail: medven@olimp.irb.hr From jkl@ccl.net Tue Sep 19 11:47:45 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA11405; Tue, 19 Sep 1995 11:45:54 -0400 Received: from relay.urz.uni-heidelberg.de for stefan@indi.aci.uni-heidelberg.de by bedrock.ccl.net (8.6.10/950822.1) id LAA27882; Tue, 19 Sep 1995 11:45:49 -0400 Received: from sun0.urz.uni-heidelberg.de by relay.urz.uni-heidelberg.de with SMTP id AA23189 (5.67b8/IDA-1.5 for ); Tue, 19 Sep 1995 17:45:30 +0200 Received: from indi.aci.uni-heidelberg.de by sun0.urz.uni-heidelberg.de (4.1/URZ-20.03.92) id AA05977; Tue, 19 Sep 95 17:45:29 +0200 Received: by indi.aci.uni-heidelberg.de (940816.SGI.8.6.9/930416.SGI) for chemistry@ccl.net id RAA17873; Tue, 19 Sep 1995 17:41:58 +0200 From: "Stefan Beyreuther" Message-Id: <9509191741.ZM17871@indi.aci.uni-heidelberg.de> Date: Tue, 19 Sep 1995 17:41:57 -0600 X-Mailer: Z-Mail (3.2.1 6apr95 MediaMail) To: chemistry@ccl.net Subject: RMS algorithm/routine Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers, I need a C routine that calculates the RMS of two different conformations of a certain molecule to incorporate it into a program. To determine the RMS - as far as I understand - one molecule has to be superimposed onto the other. How is that done? Is anybody aware of a routine or even has written one? Thanks a lot Jo _______________________________________________________________________________ Johannes Hunger Anorganisch-Chemisches Institut fon +49-6221-562565 Universitaet Heidelberg fax +49-6221-565707 69120 Heidelberg e-mail: jo@indi.aci.uni-heidelberg.de Germany _______________________________________________________________________________ From walterse@mis.finchcms.edu Tue Sep 19 13:32:46 1995 Received: from mis.finchcms.edu for walterse@mis.finchcms.edu by www.ccl.net (8.6.10/950822.1) id NAA13825; Tue, 19 Sep 1995 13:26:41 -0400 Received: from [192.217.124.142] by mis.finchcms.edu; (5.65/1.1.8.2/05May95-1218PM) id AA03163; Tue, 19 Sep 1995 12:26:55 -0500 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 19 Sep 1995 12:27:57 -0600 To: CHEMISTRY@www.ccl.net From: walterse@mis.finchcms.edu (Dr. Eric Walters) Subject: looking for 3D databases CCLers, I am looking for 3D structure databases which are accessible [read: inexpensive] for academic users. A search of the CCL archives indicates the question has been asked before, but not very satisfactorily answered. What are the choices? What do they cost? How good are they? Thanks for your input--I will summarize replies to the list. Best regards, Eric * D. Eric Walters, Ph.D., Associate Professor, Biological Chemistry * Finch University of Health Sciences/The Chicago Medical School * 3333 Green Bay Road, North Chicago, IL 60064 * ph 708-578-3000, x-498;fax 708-578-3240; email: walterse@mis.finchcms.edu * "A man would do nothing if he waited until he could do it so well that * no one would find fault with what he had done." --Cardinal Newman * ***** note that our e-mail address has changed slightly! ***** From MAILER-DAEMON@www.ccl.net Tue Sep 19 16:17:49 1995 Received: from schiele for MAILER-DAEMON@www.ccl.net by www.ccl.net (8.6.10/950822.1) id QAA17423; Tue, 19 Sep 1995 16:11:49 -0400 Received: by schiele (950215.SGI.8.6.10/940406.SGI.AUTO) for chemistry@www.ccl.net id WAA21612; Tue, 19 Sep 1995 22:11:31 +0200 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9509192211.ZM21610@schiele> Date: Tue, 19 Sep 1995 22:11:28 -0600 Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.1 6apr95 MediaMail) To: chemistry@www.ccl.net Subject: ANNOUNCE: Free Chemistry Software Tools Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit Version 1.2.1 of the CACTVS tools collection has been released. This is a collection of Tcl/Tk-based scripts running on a generic chemistry-aware data manager program. Among the tools are a full-featured 2D structure editor, a 2D structure browser, an IR spectra display tool and a number of additional goodies. Information about the context of these tools as well as downloading instructions can be obtained from http://schiele.organik.uni-erlangen.de/cactvs/index.html This is a binary-only release. Precompiled executables are provided for SunOS4.1, Solaris2.4 and Irix5.3. Versions for Linux and HPUX can be expected sometime later. A number of external test users have successfully installed and run the software. However, please tell me about any problem you might encounter. -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From jkl@ccl.net Tue Sep 19 17:17:49 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id RAA18880; Tue, 19 Sep 1995 17:08:32 -0400 Received: from seciu.uy for fer@bilbo.edu.uy by bedrock.ccl.net (8.6.10/950822.1) id RAA01616; Tue, 19 Sep 1995 17:08:29 -0400 Received: from bilbo.edu.uy by seciu.uy with smtp (Smail3.1.29.1 #11) id m0sv9qs-000m4SC; Tue, 19 Sep 95 18:05 GMT-3:00 Received: by bilbo.edu.uy (AIX 3.2/UCB 5.64/4.03) id AA18908; Tue, 19 Sep 1995 18:02:53 -0300 Date: Tue, 19 Sep 1995 18:02:53 -0300 (TZ ) From: Fernando Vila To: List CC Subject: Casimir operators Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters; some time ago I began studying the unitary group approach to calculate Hamiltonian matrix elements. I'm using "The Unitary Group in Quantum Chemistry" F.A. Matsen & R. Pauncz. The question is that the definition of the Casimir operators in terms of the unitary group generators is rather confuse. Apparently there is a type mismatch in the book. C2 = sum from r,s E sub rs E sub sr with r=s (??!!) Any hint or the correct definition will be very acknowledged. Yours, Fernando ******************************************************************************* Fernando Vila Catedra de Quimica Cuantica Tel. +(5982)941860 Facultad de Quimica Fax +(5982)941906 Gral.Flores 2124, C. C. 1157 E-mail fer@bilbo.edu.uy Montevideo 11800, URUGUAY WWW http://bilbo.edu.uy/MTC-Lab.html ******************************************************************************* From jkl@ccl.net Tue Sep 19 17:22:41 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id RAA18699; Tue, 19 Sep 1995 17:02:57 -0400 Received: from bock.ucs.ualberta.ca for decker@jcvsparc.chem.ualberta.ca by bedrock.ccl.net (8.6.10/950822.1) id RAA01534; Tue, 19 Sep 1995 17:02:56 -0400 Received: from jcvsparc.chem.ualberta.ca by bock.ucs.ualberta.ca with ESMTP (8.6.5/UA3.0.0June95) id PAA00434 for ; Tue, 19 Sep 1995 15:02:44 -0600 Received: (from decker@localhost) by jcvsparc.chem.ualberta.ca (8.6.9/8.6.9) id PAA05407 for chemistry@ccl.net; Tue, 19 Sep 1995 15:21:26 -0600 Date: Tue, 19 Sep 1995 15:21:26 -0600 From: Stephen Decker Message-Id: <199509192121.PAA05407@jcvsparc.chem.ualberta.ca> To: chemistry@ccl.net Subject: Gamess Normal Mode Animation Dear Gamess Users and CCLers in general, I am currently using Gamess for geometry optimizations, transition state optimizations, and frequency calculations in order to deduce a reaction mechanism. I am always having to look at the vibrational modes, currently I am using molplt to get a static picture of the modes (ie. arrows), however it would be much nicer to be able to animate the modes and be able to rotate the molecule in real-time via the mouse, instead of using keyboard commands. My question is this, does anyone know of, or is currently using, a good program, preferably shareware, to animate vibrations using Gamess output directly, with little or no modification? Something similar to KGNGRAF for HONDO and GAUSSIAN92, would be great. I am currently using a SunSparc2 workstation running SunOs 4.1.3, not Solarius anyways. But I also have access to a few IBM RS6000s. So a program running on either of these platforms would be greatly appreciated. Thanks, Stephen Decker Dept. of Chem Univ. of Alberta decker@jcvsparc.chem.ualberta.ca From jomal@dfq.ufrj.br Tue Sep 19 17:47:50 1995 Received: from bach.iq.ufrj.br for jomal@dfq.ufrj.br by www.ccl.net (8.6.10/950822.1) id RAA19527; Tue, 19 Sep 1995 17:45:11 -0400 Received: (jomal@localhost) by bach.iq.ufrj.br (8.6.12/8.3) id SAA13806; Tue, 19 Sep 1995 18:45:14 GMT Date: Tue, 19 Sep 1995 18:45:14 GMT From: "Joao Otavio M.A. Lins / DFQ-IQ-UFRJ" Message-Id: <199509191845.SAA13806@bach.iq.ufrj.br> To: CHEMISTRY@www.ccl.net Subject: GAMESS/US->UK Hi, Could somebody out there help me to get a program suitable to convert the GAMESS/US output to the UK version, so I could use the MolDen program to visualize my results? Thanks in advance, Joao O.M.A. Lins Quantum Chemistry Group ______________________________________________________________________ Instituto de Quimica da U.F.R.J. email: jomal@dfq.ufrj.br Centro de Tecnologia, bloco A, sala 412 voice: +55-21-590-9890 Cidade Universitaria fax : +55-21-290-4746 21949-900 - Rio de Janeiro - RJ BRAZIL ______________________________________________________________________ From rosas@irisdav.chem.vt.edu Tue Sep 19 20:17:52 1995 Received: from irisdav.chem.vt.edu for rosas@irisdav.chem.vt.edu by www.ccl.net (8.6.10/950822.1) id UAA20728; Tue, 19 Sep 1995 20:08:39 -0400 Received: by irisdav.chem.vt.edu (940816.SGI.8.6.9/940406.SGI) for chemistry@www.ccl.net id UAA24435; Tue, 19 Sep 1995 20:07:49 -0400 From: "Victor M. Rosas Garcia" Message-Id: <9509192007.ZM24433@irisdav.chem.vt.edu> Date: Tue, 19 Sep 1995 20:07:45 -0400 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Calculation of entropy Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi guys, I've been using AM1 to calculate vibrational frequencies of some zwitterions and ammonium salts, both in vacuo and using COSMO (I'm running MOPAC93 R2). I need this vibrational frequencies because I want to calculate the entropic change of the system so I can get the free energy. I've had some problems because I obtain negative frequencies when there shouldn't be any (all my conformers are supposed to be ground states) and I've already posted here in the CCL a summary of the problems I found and the strategies I followed to get rid of the problem. In my summary I stated that I was able to eliminate the negative frequencies in 80% of the cases, which means that I still have a few conformers with negative frequencies. So, my question is what should I do in this case? Drop the conformers from the entropy calculation? In most cases the problematic conformers account for less than 1% of the population (after a quick-and-dirty calculation of "Boltzmann factors" using only the enthalpies). Or should I include those conformers in the calculation thinking that the small negative vibrational frequencies will be "diluted" by all the other frequencies? Any input will be greatly appreciated. Victor -- ----------------------------------------------------------------------- Victor M. Rosas Garcia * "How can we contrive to be rosas@irisdav.chem.vt.edu * at once astonished at the Virginia Tech doesn't necessarily share * world and yet at home in it?" the opinions you just read. * G. K. Chesterton -------------------------------------------------------------------------