From muguet@poly.polytechnique.fr Thu Jun 27 08:26 EDT 1996 Received: from polytechnique.polytechnique.fr for muguet@poly.polytechnique.fr by www.ccl.net (8.7.5/950822.1) id IAA01227; Thu, 27 Jun 1996 08:26:32 -0400 (EDT) Received: from poly.polytechnique.fr (tCehI2gji/111H6tNmW/wkdyDYpm6aMD@poly.polytechnique.fr [129.104.252.1]) by polytechnique.polytechnique.fr (8.6.12/8.6.12) with ESMTP id OAA18272 for ; Thu, 27 Jun 1996 14:29:19 +0200 Received: (from muguet@localhost) by poly.polytechnique.fr (8.6.10/8.6.6) id OAA06598 for CHEMISTRY@www.ccl.net; Thu, 27 Jun 1996 14:27:06 +0200 Date: Thu, 27 Jun 1996 14:27:06 +0200 From: muguet francis Message-Id: <199606271227.OAA06598@poly.polytechnique.fr> To: CHEMISTRY@www.ccl.net Subject: MCSCF freq. + scaling factors Content-Type: text Content-Length: 1588 Status: RO Dear CCL Netters CHEMISTRY@www.ccl.net Ref: CAS vs HF frequencies, vibration scaling factors, I would like to add my grain of salt to these 2 threads. 1/ I would tend to think that MCSCF ( and then CAS ) frequencie are much better than HF and ALSO MP2. In the case, where static correlation is important, no doubt MCSCF is better. It has been argued (in the CCL discussion) than MP2 might be better to describe dynamic correlation, why ? In fact, I begun to be suspicious of MP2 schemes, when I realized that most MP2 energy is coming from the highest virtual MOs, which feature extremely bizarre contours ( plot them !) and also very large MO coefficients. 2/ For frequencies computed within the harmonic approximation, scaling factors might correct both for lack of proper correlation treatment,and lack of anharmonicity. It is safer, whenever possible, to try to separate these 2 issues. In fact MP2 frequencies, often seem better than MCSCF frequencies but this might come from a compensation of error with anharmonicity. See my WWW paper : URL : http://yvette.ensta.fr/~muguet/papers/ecc2.html Francis ====================================================================== Francis F. Muguet Ph.D Research Scientist L.O.A Ecole Polytechnique - ENSTA Centre de l'Yvette 91120 PALAISEAU FRANCE Ph: (33) (1) 60.10.03.18 ext. 12.76 Fax: (33) (1) 60.10.60.85 E-mail : muguet@poly.polytechnique.fr *or* muguet@enstay.ensta.fr Web : http://yvette.ensta.fr/~muguet ===================================================================== From muguet@poly.polytechnique.fr Thu Jun 27 08:26 EDT 1996 Received: from polytechnique.polytechnique.fr for muguet@poly.polytechnique.fr by www.ccl.net (8.7.5/950822.1) id IAA01227; Thu, 27 Jun 1996 08:26:32 -0400 (EDT) Received: from poly.polytechnique.fr (tCehI2gji/111H6tNmW/wkdyDYpm6aMD@poly.polytechnique.fr [129.104.252.1]) by polytechnique.polytechnique.fr (8.6.12/8.6.12) with ESMTP id OAA18272 for ; Thu, 27 Jun 1996 14:29:19 +0200 Received: (from muguet@localhost) by poly.polytechnique.fr (8.6.10/8.6.6) id OAA06598 for CHEMISTRY@www.ccl.net; Thu, 27 Jun 1996 14:27:06 +0200 Date: Thu, 27 Jun 1996 14:27:06 +0200 From: muguet francis Message-Id: <199606271227.OAA06598@poly.polytechnique.fr> To: CHEMISTRY@www.ccl.net Subject: MCSCF freq. + scaling factors Content-Type: text Content-Length: 1588 Status: RO Dear CCL Netters CHEMISTRY@www.ccl.net Ref: CAS vs HF frequencies, vibration scaling factors, I would like to add my grain of salt to these 2 threads. 1/ I would tend to think that MCSCF ( and then CAS ) frequencie are much better than HF and ALSO MP2. In the case, where static correlation is important, no doubt MCSCF is better. It has been argued (in the CCL discussion) than MP2 might be better to describe dynamic correlation, why ? In fact, I begun to be suspicious of MP2 schemes, when I realized that most MP2 energy is coming from the highest virtual MOs, which feature extremely bizarre contours ( plot them !) and also very large MO coefficients. 2/ For frequencies computed within the harmonic approximation, scaling factors might correct both for lack of proper correlation treatment,and lack of anharmonicity. It is safer, whenever possible, to try to separate these 2 issues. In fact MP2 frequencies, often seem better than MCSCF frequencies but this might come from a compensation of error with anharmonicity. See my WWW paper : URL : http://yvette.ensta.fr/~muguet/papers/ecc2.html Francis ====================================================================== Francis F. Muguet Ph.D Research Scientist L.O.A Ecole Polytechnique - ENSTA Centre de l'Yvette 91120 PALAISEAU FRANCE Ph: (33) (1) 60.10.03.18 ext. 12.76 Fax: (33) (1) 60.10.60.85 E-mail : muguet@poly.polytechnique.fr *or* muguet@enstay.ensta.fr Web : http://yvette.ensta.fr/~muguet ===================================================================== From irikura@ENH.NIST.GOV Tue Jun 25 09:22 EDT 1996 Received: from ENH.NIST.GOV for irikura@ENH.NIST.GOV by www.ccl.net (8.7.5/950822.1) id JAA18705; Tue, 25 Jun 1996 09:22:11 -0400 (EDT) Received: from h178075 (h178075.nist.gov) by ENH.NIST.GOV (PMDF V5.0-5 #10952) id <01I6BK3BRNDS00BPU5@ENH.NIST.GOV>; Tue, 25 Jun 1996 09:23:05 -0400 (EDT) Date: Tue, 25 Jun 1996 09:21:30 -0400 From: Karl Irikura Subject: free program to convert stick spectrum to gaussians or lorentzians X-Sender: irikura@enh.nist.gov To: chemistry@www.ccl.net Cc: smillefiori@dipchi.unict.it Message-id: <01I6BK3BXJKY00BPU5@ENH.NIST.GOV> MIME-version: 1.0 X-Mailer: Windows Eudora Version 2.1.1 Content-transfer-encoding: 7BIT Content-Type: text/plain; charset="us-ascii" Content-Length: 1252 Status: RO This small program is intended to convert the "stick" spectra produced by computational methods into synthetic spectra with realistic linewidths. No graphics is produced, just a file of (x,y) points that must be plotted using some other means. A sample input file is included in the zip file SYNSPEC. Interactive user input is 1. The desired peakshape (0=gaussian, 1=lorentzian) 2. The linewidth (in whatever units are used in SYNSPEC.INP) 3. The energy (or wavelength) range to calculate in the simulated spectrum 4. The desired interval between successive points The program has been upload to CCL in the directory /pub/chemistry/software/MS-DOS/synthetic-spectrum i.e., you can retrieve it as: ftp://www.ccl.net/pub/chemistry/software/MS-DOS/synthetic-spectrum or gopher://www.ccl.net:73/11/software/MS-DOS/synthetic-spectrum or get there view CCL Web page: http://www.ccl.net/chemisty.html Thanks to Jan L. for his help! Karl I. ---------------------------------------------- Dr. Karl K. Irikura Physical and Chemical Properties Division National Institute of Standards and Technology Gaithersburg, MD 20899 voice: 301-975-2510 fax: 301-975-3670 e-mail: irikura@enh.nist.gov ---------------------------------------------- From ccluser@chu.chem.nthu.edu.tw Fri Jun 28 09:50 EDT 1996 Received: from chu.chem.nthu.edu.tw for ccluser@chu.chem.nthu.edu.tw by www.ccl.net (8.7.5/950822.1) id JAA06986; Fri, 28 Jun 1996 09:50:40 -0400 (EDT) Received: by chu.chem.nthu.edu.tw (AIX 3.2/UCB 5.64/4.03) id AA17913; Fri, 28 Jun 1996 21:49:19 +0900 From: Message-Id: <9606281249.AA17913@chu.chem.nthu.edu.tw> Subject: DFT input To: chemistry@www.ccl.net Date: Fri, 28 Jun 96 21:49:19 TAIDT X-Mailer: ELM [version 2.4dev PL17] Content-Type: text Content-Length: 978 Status: RO -- Dear freinds, I got a question when I tried to run DFT using gaussian 94: I ran three kinds of input as follows, (1) #n b3lyp/sto-3g iop(5/45=10000800) iop(5/46=02000720) iop(5/47=01900810) (2) #n blyp/sto-3g iop(5/45=10000800) iop(5/46=02000720) iop(5/47=01900810) (3) #n b3lyp/sto-3g Why both (1) and (2) give the same energy results but differ from that of (3) ? And which input is the right one? Please e-mail me using the following e-mail adress Thanks a lot in advance. ========================================================================== May May Lin | E-mail: ccluser@chu.chem.nthu.edu.tw Department of chemistry | National Tsing Hua University | Phone: 886-35-721634 Hsinchu, Taiwan 30043 | Fax: 886-35-711082 ===================================================================== From ccluser@chu.chem.nthu.edu.tw Mon Jul 1 00:10 EDT 1996 Received: from chu.chem.nthu.edu.tw for ccluser@chu.chem.nthu.edu.tw by www.ccl.net (8.7.5/950822.1) id AAA17479; Mon, 1 Jul 1996 00:09:59 -0400 (EDT) Received: by chu.chem.nthu.edu.tw (AIX 3.2/UCB 5.64/4.03) id AA15362; Mon, 1 Jul 1996 12:08:32 +0900 From: Message-Id: <9607010308.AA15362@chu.chem.nthu.edu.tw> Subject: DFT input To: chemistry@www.ccl.net Date: Mon, 1 Jul 96 12:08:31 TAIDT Cc: lin@chu.chem.nthu.edu.tw X-Mailer: ELM [version 2.4dev PL17] Content-Type: text Content-Length: 970 Status: RO Dear freinds, I got a question when I tried to run DFT using gaussian 94: I ran three kinds of input as follows, (1) #n b3lyp/sto-3g iop(5/45=10000800) iop(5/46=02000720) iop(5/47=01900810) (2) #n blyp/sto-3g iop(5/45=10000800) iop(5/46=02000720) iop(5/47=01900810) (y3) #n b3lyp/sto-3g Why both (1) and (2) give the same energy results but differ from that of (3)? And which input is the right one? Please e-mail me using the following e-mail adress Thanks a lot in advance. ===================================================================== May-May Lin | E-mail: ccluser@chu.chem.nthu.edu.tw Department of chemistry | National Tsing Hua University | Phone: 886-35-721634 Hsinchu, Taiwan 30043 | Fax: 886-35-711082 ===================================================================== From PDU@mbcl.rutgers.edu Mon Jul 1 08:21 EDT 1996 Received: from OCELOT.RUTGERS.EDU for PDU@mbcl.rutgers.edu by www.ccl.net (8.7.5/950822.1) id IAA21905; Mon, 1 Jul 1996 08:21:55 -0400 (EDT) Received: from mbcl.rutgers.edu by mbcl.rutgers.edu (PMDF #12194) id <01I6JVKZJ6FK984M80@mbcl.rutgers.edu>; Mon, 1 Jul 1996 08:18 EDT Date: Mon, 1 Jul 1996 08:18 EDT From: PDU@mbcl.rutgers.edu Subject: R:bioinformatics group? To: chemistry@www.ccl.net Message-id: <01I6JVKZJ6FK984M80@mbcl.rutgers.edu> X-Envelope-to: chemistry@www.ccl.net X-VMS-To: IN%"chemistry@www.ccl.net" Content-Type: text Content-Length: 863 Status: RO Phil Xiang mentioned identifying function from sequence as a task of bioinformatics. This is indeed very important for those of us who work in industry and would like to "clone" new sequences of desired function by computer. For example, by using a highly conserved sequence pattern of G protein-coupled receptors, one may fish out fragments of novel GPCR receptor sequences. Most scoring matrices for sequence alignment are probably derived from mutation patterns of water soluble proteins. Since membrane bound receptors may have different mutations (lipophilic amino acids for lipophilic amino acids) than water soluble proteins (hydrophilic for hydrophilic), using these scoring matrices may fail to identify low homology sequences in similarity search. My question is -- are there scoring matrices derived specifically for membrane bound receptors? From f537pudm@mbox.tu-graz.ac.at Tue Jun 25 07:22 EDT 1996 Received: from mbox.tu-graz.ac.at for f537pudm@mbox.tu-graz.ac.at by www.ccl.net (8.7.5/950822.1) id HAA18200; Tue, 25 Jun 1996 07:22:00 -0400 (EDT) Received: from fchtapc11 (fchtapc11.tu-graz.ac.at) by mbox.tu-graz.ac.at with SMTP id AA03091 (5.67c/IDA-1.5t for ); Tue, 25 Jun 1996 13:22:24 +0200 Message-Id: <199606251122.AA03091@mbox.tu-graz.ac.at> Comments: Authenticated sender is From: "Guenter Pudmich" To: CHEMISTRY@www.ccl.net Date: Tue, 25 Jun 1996 13:24:56 +0000 Subject: Re: graph to table software Priority: normal X-Mailer: Pegasus Mail for Windows (v2.23) Content-Type: text Content-Length: 565 Status: RO >hi, > does anybody know of a software package (public domain) >that converts graphs to tables? Windig is a free data digitizer with a convenient user interface working under windows 3.1. It imports common graphic formats and works with twain compatible scanners. Search it under "/cica/win3/desktop/windig20.zip" (or similar) on your next ftp-server. Best regards, Guenter Guenter Pudmich f537pudm@mbox.tu-graz.ac.at Institute of Chemical Technology of Inorganic Materials Technical University of Graz Tel. +43 316 873 8293 Fax +43 316 873 8769 From rene@crys.chem.uva.nl Mon Jul 1 02:52 EDT 1996 Received: from sahara.chem.uva.nl for rene@crys.chem.uva.nl by www.ccl.net (8.7.5/950822.1) id CAA17825; Mon, 1 Jul 1996 02:52:06 -0400 (EDT) Received: from crys.chem.uva.nl (mimi.chem.uva.nl [145.18.128.36]) by sahara.chem.uva.nl (8.6.12/8.6.12) with SMTP id JAA22452 for ; Mon, 1 Jul 1996 09:00:50 +0200 Received: by crys.chem.uva.nl (MX V4.2 VAX) id 1; Mon, 01 Jul 1996 08:53:46 MET-1MDT From: Date: Mon, 01 Jul 1996 08:51:03 MET-1MDT To: chemistry@www.ccl.net Message-ID: <009A4AB2.E62BB820.1@crys.chem.uva.nl> Subject: Conference Molec. Modelling, Amsterdam 9-10 september 1996 Content-Type: text Content-Length: 3180 Status: RO CONFERENCE - MOLECULAR MODELLING OF CHEMICALS AND MATERIALS Amsterdam, The Netherlands, September 9-10, 1996 Society's demands for affordable chemicals and materials with novel or enhanced performance characteristics continue to grow as exciting new application areas are recognised, and the requirements in existing areas become increasingly more stringent. Molecular modelling and simulation techniques have an important role to play in these developments by helping to provide a more focussed, molecular-level understanding of chemical products and processes, which in turn can help to guide future experimental work. This meeting, organised by the Molecular Graphics and Modelling Society and the University of Amsterdam, will bring together theoreticians and experimentalists from a variety of relevant fields to discuss molecular modelling approaches in chemicals and materials research, and is expected to be of value to scientists in industry and academe alike. Topics covered by the meeting will include: - Catalysis and Surfaces - Fluids and Interfaces - Polymers Speakers will include: Prof. E.J. Baerends (Amsterdam), Prof. J.H.R. Clarke (UMIST), Dr. J. Gale (London), Prof. W.A. Goddard (Caltech), Dr. F. Muller-Plathe (Mainz), Prof. K. Roberts (Strathclyde), Prof. R. Van Santen (Eindhoven), Dr. B. Smit (Shell) and Prof. D. Tildesley (Imperial, London) Organising Committee : Dr. M.A. King (Shell) Chairman; Dr. E.A. Colbourn (Oxford Materials Ltd.); Dr. M.G.B. Drew (University of Reading); Dr. A.M. Brouwer (University of Amsterdam) Local Organiser; Dr. R. Peschar (University of Amsterdam) Local Organiser Program The program will consist of invited lectures and oral presentations. On both days there will be a session of ca. three hours which will include buffet lunch, poster session and a commercial exhibition, all in the same location. Abstracts (one page A4, ready for reproduction) of contributed talks or posters should be sent to Dr. A.M. Brouwer at the address below. If you wish to present your work orally please ensure that your abstract is in our possession before July 15, and please add a brief description of your position and scientific career. The selection of oral presentations will be made before July 30. The committee will favour contributions from younger scientists. Registration The conference fee is DFl. 300 for regular participants, DFl. 175 for students. For registration after July 15, the fee is increased by DFl 50. To qualify for the reduced rate students must include a letter from their research supervisor. A limited number of student bursaries will be available. The registration fee includes a book of abstracts, lunches, coffee and tea during breaks, and an informal dinner on monday evening. Registration and hotel reservation forms are available at the Conference Web site: http://krop.chem.uva.nl/mgms/ or will be sent upon request to the (E-mail) address given below. Send abstracts and registration form to: Dr. A.M. Brouwer University of Amsterdam, Laboratory of Organic Chemistry Nieuwe Achtergracht 129, NL-1018 WS Amsterdam, The Netherlands Fax 31 (0)20 5255670, E-mail: mgms@chem.uva.nl From tj@eecs.uic.edu Tue Jun 25 12:32 EDT 1996 Received: from mail.eecs.uic.edu for tj@eecs.uic.edu by www.ccl.net (8.7.5/950822.1) id MAA20228; Tue, 25 Jun 1996 12:32:01 -0400 (EDT) Received: from ernie.eecs.uic.edu (tj@ernie.eecs.uic.edu [128.248.176.24]) by mail.eecs.uic.edu (8.7.5/8.7.5) with ESMTP id LAA24508 for ; Tue, 25 Jun 1996 11:32:00 -0500 (CDT) Received: (tj@localhost) by ernie.eecs.uic.edu (8.6.10/8.6.10) id LAA29901 for chemistry@www.ccl.net; Tue, 25 Jun 1996 11:31:58 -0500 From: tj ODonnell Message-Id: <199606251631.LAA29901@ernie.eecs.uic.edu> Subject: PS390 free to a good home To: chemistry@www.ccl.net (CCL) Date: Tue, 25 Jun 1996 11:31:57 -0500 (CDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Content-Length: 237 Status: RO There is an Evans & Sutherland PS390 graphics system available FREE from Searle, located in the Chicago area. If you can come get it, its yours! If you have questions, please address them to: Dale Spangler spangler@searle.monsanto.com From cwescott@indigo.aspensystems.com Mon Jul 1 16:52 EDT 1996 Received: from fuji.ixl.net for cwescott@indigo.aspensystems.com by www.ccl.net (8.7.5/950822.1) id QAA24722; Mon, 1 Jul 1996 16:52:09 -0400 (EDT) Received: from indigo.aspensystems.com (indigo.aspensystems.com [199.173.189.102]) by fuji.ixl.net (8.6.11/8.6.11) with ESMTP id QAA05758 for <@mailhost.ixl.net:chemistry@www.ccl.net>; Mon, 1 Jul 1996 16:45:47 -0400 Received: by indigo.aspensystems.com (940816.SGI.8.6.9/930416.SGI) for chemistry@www.ccl.net id QAA01697; Mon, 1 Jul 1996 16:48:26 -0400 Date: Mon, 1 Jul 1996 16:48:26 -0400 From: cwescott@indigo.aspensystems.com (cwescott) Message-Id: <199607012048.QAA01697@indigo.aspensystems.com> Subject: MOPAC 7 Apparently-To: chemistry@www.ccl.net Content-Type: text Content-Length: 210 Status: RO Greetings: What is the difference between the public domain version of MOPAC 7 and the version distributed by the Quantum Chemistry Program Exchange? Thanks, Charles Wescott cwescott@indigo.aspensystems.com From owner-chemistry@ccl.net Sun Jun 30 20:07 EDT 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id UAA17100; Sun, 30 Jun 1996 20:07:54 -0400 (EDT) Received: from auric.chem.csiro.au for D.Winkler@chem.csiro.au by bedrock.ccl.net (8.7.5/950822.1) id UAA25749; Sun, 30 Jun 1996 20:07:51 -0400 (EDT) Received: from [138.194.40.190] (mac-40190.chem.csiro.au) by auric.chem.csiro.au with SMTP id AA12712 (5.67b/IDA-1.5 for chemistry@ccl.net); Mon, 1 Jul 1996 10:06:13 +1000 From: Date: Mon, 1 Jul 1996 10:06:13 +1000 X-Sender: win097@auric.chem.csiro.au Message-Id: Mime-Version: 1.0 Apparently-To: Content-Type: text/plain; charset="us-ascii" Content-Length: 1163 Status: RO Australian Science - Australia's Future Date: Mon, 1 Jul 1996 10:07:43 +1000 To: chemistry@ccl.net From: D.Winkler@chem.csiro.au (Dr. Dave Winkler) Subject: Summary: Laplacian of Electron Density Thanks very much to all who responded. Many people pointed to Prof. Bader's work and his PROAIM and other software packages, sent me his email address (bader@mcmaster.ca) or home page URL: http://www.chemistry.mcmaster.ca/faculty/bader.html The home page contains an interesting summary of the AIM methods. One of Bader's group, Dr. Tang (ttang@babbage.Chemistry.McMaster.CA), very kindly emailed me the source for all of the programs. Ian Bytheway suggested MORPHY from Dr Paul Popelier: pla@umist.ac.uk. Martin Schuetz (teomgs@teokem.lu.se, teomgs@garm.teokem.lu.se) suggested the current version of MOLDEN can do such stuff. Cheers, Dave Dr. David A. Winkler Voice: 61-3-9542-2477 Principal Research Scientist Fax: 61-3-9543-8160 CSIRO Division of Chemicals and Polymers http://www.csiro.au Private Bag 10,Rosebank MDC, Clayton, Australia http://www.wark.csiro.au