From oesterei@hrz.ba-freiberg.de Tue May 31 07:42:44 1994 Received: from orion.hrz.ba-freiberg.de for oesterei@hrz.ba-freiberg.de by www.ccl.net (8.6.4/930601.1506) id HAA16582; Tue, 31 May 1994 07:02:55 -0400 Message-Id: <199405311102.HAA16582@www.ccl.net> Received: by orion.hrz.ba-freiberg.de (16.6/15.6) id AA12063; Tue, 31 May 94 13:00:30 +0200 From: Ralf Oestereich Subject: GAMESS: gradient out of range error To: chemistry@ccl.net (Computer Chemistry List) Date: Tue, 31 May 94 13:00:29 MESZ Mailer: Elm [revision: 66.25] Dear netters, we have the following problem with GAMESS (US): While calculating the molecule: H3C . Cl \ . Cl.....Si --------------Si xxx Cl x \ Cl CH3 with a 3-21G basis set, using no symmetrie (C1), GAMESS terminates after a few hours with: MAXIMUM GRADIENT = 3.5926839 RMS GRADIENT = 1.1734616 0OPTIMIZATION ABORTED. -- GRADIENT OUT OF RANGE -- MAXIMUM ALLOWED FORCE (FMAXT) = 1.000 EXECUTION OF GAMESS TERMINATED ABNORMALLY AT Mon May 30 13:29:14 1994 As input with use coordinates which are optimzed with ALCHEMEY (PC-Windows Version), and then simply translate them, so that the first Silicon lies at 0/0/1.52. At least out input-file: $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE COORD=UNIQUE $END $CONTRL PLTORB=.TRUE. MOLPLT=.TRUE. EXETYP=RUN $END $SYSTEM TIMLIM=6000 MEMORY=300000 $END $BASIS GBASIS=N21 NGAUSS=3 $END $GUESS=HUCKEL $END $STATPT NSTEP=200 $END $DATA MethylChlor2-Sil-Sil-MethylChlor2 RHF/3-21G, Symmetrie C1 C1 SILICON 14.0 0.0000 0.0000 0.8094 SILICON 14.0 2.2068 0.2512 -0.7219 CHLOR 17.0 -0.4898 -0.7698 -0.6029 CARBON 6.0 -0.0041 -0.4822 1.8261 CARBON 6.0 2.2029 0.9573 -2.4745 CHLOR 17.0 2.7256 0.9298 0.0391 HYDROGEN 1.0 1.6782 1.9252 -2.4824 HYDROGEN 1.0 1.6753 0.2673 -3.1496 HYDROGEN 1.0 3.2307 1.105 -2.843 HYDROGEN 1.0 -1.0186 -0.6726 2.1871 HYDROGEN 1.0 0.4482 0.3304 2.421 HYDROGEN 1.0 0.6092 -1.3903 1.9685 CHLOR 17.0 -0.5346 0.9436 -0.1505 CHLOR 17.0 2.7156 -0.7913 -0.6104 $END What must we change, to calculate the molecule? Is our basis-set okay? Why does GAMESS terminate, what does it mean, if the gradient vector is to big? I hope someone is able to help us! Please send mail to oesterei@orion.hrz.ba-freiberg.de Thanks in advance, Ralf From mckelvey@Kodak.COM Tue May 31 08:42:43 1994 Received: from Kodak.COM for mckelvey@Kodak.COM by www.ccl.net (8.6.4/930601.1506) id IAA16972; Tue, 31 May 1994 08:14:54 -0400 From: Received: from NTPROF.DECnet MAIL11D_V3 by Kodak.COM (5.61+/2.1-Eastman Kodak) id AA11203; Tue, 31 May 94 08:17:14 -0400 Date: Tue, 31 May 94 08:17:10 -0400 Reply-To: mckelvey@Kodak.COM Message-Id: <9405311217.AA11203@Kodak.COM> To: osc@Kodak.COM Subject: Initial Hessians Netters: The question has been raised as to the best initial Hessian for ab initio calculations. Someone commented "what could be better than the analytical ab initio hessian at the starting geometry?" Others suggest from semiempirical methods. I have another point of view. What I have found to be the most useful, assuming that a ground state is sought, is to be sure that a reasonable starting geometry with a reliably positive definite hessian is obtained. I have found that the source of the hessian is not as critical when there are no critical, low energy torsions. Things are quite different when there are low energy torsions. The program I use almost exclusively for geometries is GAUSSIAN-92, and I have determined a rather robust strategy for starting off an ab initio run. First the initial geometry is obtained and optimised in GAUSSIAN using PM3. Next the ab initio run is started using OPT=MNDOFC iop(4/20=7). (For the iop overrides the comments in fortran source for the 400 links must be consulted for all the details. The provided documentation leaves some of this out.) The iop overide is the critical issue here... By default you will get an AM1 hessian, regardless of whether or not AM1 or PM3 is initially used for an initial geometry.... It is vital that the initial geometry and the initial hessian be determined BY THE SAME METHOD. This is true, regardless of the method used! (Exceptions can certainly be found when high level basis sets are used in ab initio determinations.) For example, when torsion angles differ by 20-30 degrees between PM3 and AM1, and the initial geometry comes from PM3 (RPM3) and OPT=MNDOFC alone is used, the AM1 hessian can lead to major grief. I have found that for floppy molecules this approach works extremely well, and thus should work for all molecules.... It assumed that you are using the semi-empirical method or basis set of your choice. John McKelvey Eastman Kodak McKelvey@Kodak.Com From rs0thp@RohmHaas.Com Tue May 31 09:42:46 1994 Received: from monte.br.RohmHaas.Com for rs0thp@RohmHaas.Com by www.ccl.net (8.6.4/930601.1506) id JAA17575; Tue, 31 May 1994 09:01:31 -0400 Received: by monte.br.RohmHaas.Com (AIX 3.2/UCB 5.64/4.03) id AA19544; Tue, 31 May 1994 08:59:56 -0400 From: rs0thp@RohmHaas.Com (Dr. Tom Pierce) Message-Id: <9405311259.AA19544@monte.br.RohmHaas.Com> Subject: Re: CCL:Real-Time Conference To: h.rzepa@ic.ac.uk (Henry Rzepa) Date: Tue, 31 May 1994 08:59:55 +22305458 (EDT) Cc: Chemistry@ccl.net In-Reply-To: <9405280936.AA04797@cscmgb.cc.ic.ac.uk> from "Henry Rzepa" at May 28, 94 09:45:08 am X-Mailer: ELM [version 2.4 PL13] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1433 Previously, Henry Rzepa wrote: > > As for www94, the consensus was that we all needed > to meet in person for precisely the > feedback. The most successful aspect were the > workshops with round table discussions. > Of course this format may not be needed for > a purely chemical discussion! Perhaps the model > of the chemistry www94 workshop could be used. > About 8 people contributed papers, but did > not actually attend. The discusion amongst > the physically present participants revolved around > issues raised in part by these papers. > > We hope to arrange a "prototype" conference before the fall. If this works, > we could try a larger scale experiment? Dear Prof. Rzepa and potential participants, I propose that a 'larger scale' experiment be run at a ACS symposia. I was *volunteered* to help organize a "Chemistry on the Infobahn" Symposia for the Computers and Chemistry Division of the American Chemical Society. My hope is that much of this can be electronic. The symposia is scheduled for Fall 1995 (Aug 27th-Sept 1.) and will physically be in Chicago, Illnois USA. This is too long from now for a "prototype test", but it is soon enough to plan for a larger implementation. If Prof. Rzepa is willing, perhaps we could jointly make this work? -- Sincerely, Thomas Pierce - THPierce@RohmHaas.Com - Computational Chemist "These opinions are those of the writer and not the Rohm and Haas Company." From smb@smb.chem.niu.edu Tue May 31 12:42:53 1994 Received: from mp.cs.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.6.4/930601.1506) id MAA21088; Tue, 31 May 1994 12:05:51 -0400 Received: from cz2.chem.niu.edu by mp.cs.niu.edu with SMTP id AA01442 (5.67a/IDA-1.5 for <@mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@ccl.net>); Tue, 31 May 1994 11:05:49 -0500 Received: from smb.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@ccl.net) id AA20461; Tue, 31 May 94 10:07:08 -0500 Received: by smb.chem.niu.edu (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:CHEMISTRY@ccl.net) id AA03212; Tue, 31 May 94 10:07:07 -0500 Date: Tue, 31 May 94 10:07:07 -0500 From: smb@smb.chem.niu.edu (Steven Bachrach) Message-Id: <9405311507.AA03212@smb.chem.niu.edu> To: CHEMISTRY@ccl.net Subject: Chemist's Email/Phone book now operational The Chemist's email/phone book is now online. It can be searched at the NIU gopher/web site. The gopher address is hackberry.chem.niu.edu port 70, the email directory is selection 11. To access the web site, the URL is http://hackberry.chem.niu.edu:70/0/webpage.html The directory can be searched by name or any other word which may identify the individuall of interest. (For those who care, the directory is actually searched using WAIS.) To submit your own entry to the directory, send an email message containined the information you want to share to chemdir@hackberry.chem.niu.edu with the subject line ADD. If you want to delete or replace your entry, use the subject line DELETE or REPLACE, respectively. Steve Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From hodgkina@vax.ox.ac.uk Tue May 31 12:47:33 1994 Received: from oxmail2.ox.ac.uk for hodgkina@vax.ox.ac.uk by www.ccl.net (8.6.4/930601.1506) id LAA20939; Tue, 31 May 1994 11:59:03 -0400 From: Received: from vax.ox.ac.uk by oxmail2.ox.ac.uk. with SMTP (PP) id <19469-0@oxmail2.ox.ac.uk.>; Tue, 31 May 1994 16:57:05 +0100 Received: by vax.ox.ac.uk (MX V4.0-1 VAX) id 1; Tue, 31 May 1994 16:58:34 +0100 Sender: hodgkina@vax.ox.ac.uk Date: Tue, 31 May 1994 16:58:31 +0100 To: CHEMISTRY@ccl.net Message-ID: <0097F42E.C08D8345.1@vax.ox.ac.uk> Subject: Mol2Mol a file translation program to be tested Dear Netters If you are interested in beta-testing a program (mol2mol) which translates a large number of chemically useful file formats please read on: Cherwell Scientific is a specialist publisher of scientific software for the Windows and Mac platforms. We publish programs in chemistry, molecular biology, genetics, statistics, image processing, and other scientific disciplines. Our programs are commercially marketed, documented and suppported, with royalties paid to the developers. The prices are in the region of $200-750. We will soon release a package running under Microsoft Windows which recognises and translates chemistry formats (about 20 and I append a list). We are keen to get the application widely tested in the next month or so. If you have a need to translate to or from any of the following formats please give me your e-mail and conventional address and I will send you a beta-copy for testing. Your comments will be extremely useful to us. We offer a small reward to beta-testers who complete reports promptly! Molecule files MOL2MOL can automatically recognize (R) and write (W) the following molecule file formats: True modeling program files: ALCHEMY I-III (Tripos Associates, Inc.) *RW SYBYL MOL -"- *RW SYBYL MOL2 -"- *RW MDL (Molecular Design Ltd.) *RW MOLIDEA (CheMicro Ltd.) *RW Desktop Molecular Modeller *RW PCMODEL (Serena Software) *RW HyperChem (HyperCube Inc) *RW MOBY (Springer) 1 *RW Brookhaven PDB (Brookhaven) *RW ChemWindow (SoftShell Int. Ltd) *RW ChemDraft (C_Graph Software) *RW Beilstein Rosdal (Softron) *R Z matrix user's free format or MOPAC #RW X-ray fractional CIF *R Cambridge FDAT *R Cambridge MODEL *R user's free format #R Cartesian user's free format #R Drawing program files: PLUTO (CSD and PC versions) W PLT (RYLAZ Products) W WIMP (Aldrich Chemical Co.) W Schakal (Univ. Freiburg) W * Recognized automatically # Insertion of a marker is necessary The conversion is made automatically, but because different programs may use different special atom or bond types (extended atoms, dummy atoms,lone electron pairs, aromatic bonds or atoms etc), MOL2MOL may sometimes prompt you for additional information. A brief summary of atom and bond types used by the different programs can be found under the appropriate headings. Best wishes Adam Hodgkin Cherwell Scientific The Magdalen Centre Oxford Science Park Oxford OX4 4GA Tel: 44-865-784800 Fax: 44-865-784801 adam.hodgkin@queens.oxford.ac.uk From agarwala@bscr.uga.edu Tue May 31 13:42:48 1994 Received: from bscr.uga.edu for agarwala@bscr.uga.edu by www.ccl.net (8.6.4/930601.1506) id NAA21856; Tue, 31 May 1994 13:37:39 -0400 From: Received: by BSCR.UGA.EDU (MX V3.3 VAX) id 13070; Tue, 31 May 1994 13:34:31 EDT Date: Tue, 31 May 1994 13:34:30 EDT To: chemistry@ccl.net Message-ID: <0097F412.40045BD0.13070@BSCR.UGA.EDU> Subject: list of positions available in CADD Dear Sir/Madam, I would like to obtain a list of positions available in computational chemistry/ molecular modeling/ computer-aided drug design. Thankyou. Atul From jerzy@tiger.jsums.edu Tue May 31 14:42:52 1994 Received: from tiger.jsums.edu for jerzy@tiger.jsums.edu by www.ccl.net (8.6.4/930601.1506) id OAA22526; Tue, 31 May 1994 14:14:43 -0400 Received: by tiger.jsums.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA06734; Tue, 31 May 94 13:16:09 -0700 Date: Tue, 31 May 94 13:16:09 -0700 From: jerzy@tiger.jsums.edu (Leszczynski) Message-Id: <9405312016.AA06734@tiger.jsums.edu> To: chemistry@ccl.net Subject: Computational Chemistry Conference Dear Colleague: We are pleased to announce the 3rd conference on CURRENT TRENDS IN COMPUTATIONAL CHEMISTRY. The symposium organized by Jackson State University will cover all areas of Computational Chemistry as well as Quantum Chemistry. The local host of the conference is US Army Engineer Waterways Experiment Station in Vicksburg. The meeting will be held at the Holiday Inn of Vicksburg (40 miles west from Jackson), Mississippi on November 11 & 12, 1994. The format consists of a series of plenary lectures and poster presentations on Friday and Saturday followed by a banquet on Saturday evening. In addition a welcoming reception and poster presentations are scheduled on Friday night. There will be talks covering applications as well as theory. We are planning to publish extended abstracts (up to 4 pages) of all invited talks and poster presentations. Original scientific contributions will be published in the special issue of the international journal "STRUCTURAL CHEMISTRY". The manuscripts should be submitted in triplicate upon the arrival at the registration desk. The submitted papers will follow the regular refereeing procedure. Enclosed are Announcement Poster, a registration form and a housing information. The deadline for registration and abstract submission is September 15, 1994. Sincerely, Jerzy Leszczynski Address:Jerzy Leszczynski, Jackson State University, Dept of Chemistry, 1400 JR Lynch St., Jackson, MS - 39217. Phone: (601) 973-3482 Fax: (601) 973-3674. E-Mail : jerzy2@iris5.jsums.edu. PROGRAM The program will include invited papers and contributed posters in all areas of Quantum and Computational Chemistry. INVITED SPEAKERS Cary F. Chabalowski US Army Ballistic Research Laboratory Jerzy Cioslowski Florida State University Gernot Frenking Philipps-Universitat Marburg Lionel Goodman Rutgers University Tom Halgren Merck Incorporation Nicholas C. Handy University of Cambridge Eluvathingal D. Jemmis University of Hyderabad Peter Kollman University of California Josef Michl University of Colorado Keiji Morokuma Emory University Steve Scheiner Southern Illionois University Per Siegbahn University of Stockholm Kenneth B. Wiberg Yale University Registration form: 3rd Conference on CURRENT TRENDS IN COMPUTATIONAL CHEMISTRY NOVEMBER 11 & 12, 1994, Jackson, Mississippi 1. NAME: MAILING ADDRESS TELEPHONE: FAX: E-MAIL: 3. If you wish to present a poster, please indicate the title below. All abstracts are due September 15, 1994 (up to 4 pages in length, presenting author underlined, photo-ready quality, in duplicate) to ensure publication in the Conference Materials. TITLE: AUTHORS: 4. Conference materials, special issue of the "STRUCTURAL CHEMISTRY", banquet and reception fee, all meals from breakfast on Friday through dinner on Saturday, cofee and refreshments are included per paid participant. Make checks payable to : JACKSON STATE UNIVERSITY, Department of Chemistry, in accord with the fee structure listed below. Registration fee before September 15, 1994, $120.00 $------- Registration fee thereafter, $ 170.00 $------- Registration fee at student discount, $50.00 $------- 5. HOUSING: The organizers will not make housing reservations. In order to reserve a room at a special conference rate of $55.00 per room call Holiday Inn of Vicksburg, 3330 Clay Street, Vicksburg, Ms-39180. Phone (601)636-4551, Fax:(601)636-4552. The reservation should be arranged with the Holiday Inn before October 15, 1994. I do ------- do not ------- plan to stay at the conference hotel. I do ------- do not ------- plan submit a paper to the special issue of "STRUCTURAL CHEMISTRY" ----------------- signature Please type all entries and return to Jerzy Leszczynski, Department of Chemistry, Jackson State University. P.O.Box 17910, Jackson, MS 39217. From MSCHRIVER@kean.ucs.mun.ca Tue May 31 17:42:53 1994 Received: from morgan.ucs.mun.ca for MSCHRIVER@kean.ucs.mun.ca by www.ccl.net (8.6.4/930601.1506) id QAA25219; Tue, 31 May 1994 16:44:18 -0400 Received: from leif.ucs.mun.ca by morgan.ucs.mun.ca with SMTP id AA09834 (5.65d3+/IDA-1.4.2+MUN1.3 for chemistry@ccl.net); Tue, 31 May 94 18:15:46 -0230 Date: Tue, 31 May 1994 18:13:56 +0200 (IST) From: "Schriver,M;Chemistry;" Subject: CCL:HyperChem To: chemistry@ccl.net Cc: mschriver@kean.ucs.mun.ca Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I've been lurking here recently and was hesitant to post but Rafael Najmanovich posted a request yesterday that struck home. Last year I wanted a software package that would 1) give publishable semi-empirical calculations on small molecules 2) be easy to use and 3) generate high quality graphics output of molecules and orbitals. After some looking around I chose HyperChem. I guess the biggest selling point for me was that AutoDesk was behind it. In all I have now spent $ 2000 [Can] on the program, up-grades and add-on modules [HyperChem 3 + ChemPlus]. I have to say that it is a very easy program package to use and it provides excellent graphics output of results. Since I consider myself barely able to appreciate what eigenvalues and eigenvectors are I took it on faith that the programmers knew what they were up to. All I wanted from the program were the energies and compositions of the frontier orbitals of small molecules and the atomic charges. The only reviews that I have seen have been fairly superficial [ex. J. Chem. Ed. (1993) A144]. To make a long story short a couple of chemists more familiar with theoret- ical chemistry that I recently talked to were so negative on the program I am seriously reconsidering publishing anything I get from the package even if it confirms my experimental results. They said that the parameterisation of the package was so poor that the only reliable results would be on the exact same molecules that HyperChem used to create the parameter files. Since I am looking at S and P in small hetercycles I was warned very strongly against using HyperChem in AM1 or PM3 calculations. They then proceded to tell me that the only reliable results would come from programs that have names that encompass half the alphabet and most of the alternate characters on the keyboard. Leaving me with the idea that these calculations should be left to the professionals. Oh well. Before I throw away my copy of HyperChem could this list please address this issue? Where are semi-empirical calculations reliable? Is there a difference between AM1 in HyperChem and AM1 in the original manuscripts? If Rafael gets any personal answers could he please post them here? Thanx in advance Mel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + M.J. Schriver, Assist. Prof., + Ph. (709) 737-8744 + + Memorial University of NFLD + Fax (709) 737-3702 + + St. John's, NFLD, Canada, A1B 3X7 + eml mschriver@kean.ucs.mun.ca + From C1790@SLVAXA.UMSL.EDU Tue May 31 18:42:50 1994 Received: from SLVAXA for C1790@SLVAXA.UMSL.EDU by www.ccl.net (8.6.4/930601.1506) id SAA26547; Tue, 31 May 1994 18:19:54 -0400 From: Received: from SLVAXA.UMSL.EDU by SLVAXA.UMSL.EDU (PMDF V4.2-11 #2503) id <01HCZWIZWKZMCWH6U1@SLVAXA.UMSL.EDU>; Tue, 31 May 1994 17:22:47 CST Date: Tue, 31 May 1994 17:22:47 -0600 (CST) Subject: FROM BILL WELSH To: CHEMISTRY@ccl.net Message-id: <01HCZWIZWUMSCWH6U1@SLVAXA.UMSL.EDU> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT JAN, IS THERE A SPECIAL LOCATION ON THE COMPUT. CHEM. BULLETIN BOARD TO POST "POSITIONS OPEN" ADS (LIKE TO ADVERTISE FOR POSTDOCS)? THANKS ... BILL From marty@ionchannel.med.harvard.edu Tue May 31 18:46:59 1994 Received: from harvard.harvard.edu for marty@ionchannel.med.harvard.edu by www.ccl.net (8.6.4/930601.1506) id RAA26172; Tue, 31 May 1994 17:45:51 -0400 Received: by harvard.harvard.edu (5.54/a0.25) (for chemistry@ccl.net) id AA24595; Tue, 31 May 94 17:45:50 EDT Received: from ionchannel.med.harvard.edu by heimdall.med.harvard.edu.med.harvard.edu (4.1/SMI-4.1) id AA10318; Tue, 31 May 94 21:41:51 GMT Received: from [134.174.159.129] by ionchannel.med.harvard.edu via SMTP (931110.SGI/920502.SGI) for @heimdall.med.harvard.edu:chemistry@ccl.net id AA22898; Tue, 31 May 94 17:45:41 -0700 Message-Id: <9406010045.AA22898@ionchannel.med.harvard.edu> X-Sender: marty@ionchannel.med.harvard.edu Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 31 May 1994 16:45:31 -0400 To: chemistry@ccl.net From: marty@ionchannel.med.harvard.edu (Marty Gallagher) Subject: chemistry moo X-Mailer: Hello, I've just discovered biomoo (the biological virtual meeting place). Does anyone know of a chemistry moo, or, better yet, a computaional chemistry/computational biology moo? Thanks, Marty ========================================================================= Martin J. Gallagher phone: (617) 432-1729 Dept. of Neurobiology fax: (617) 734-7557 Harvard Medical School E-mail: marty@ionchannel.med.harvard.edu 220 Longwood Ave Boston, MA 02115 -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran =========================================================================== From szeinfel@fox.cce.usp.br Tue May 31 19:42:50 1994 Received: from bee08.uspnet.usp.br for szeinfel@fox.cce.usp.br by www.ccl.net (8.6.4/930601.1506) id TAA27141; Tue, 31 May 1994 19:36:09 -0400 Received: from fox.cce.usp.br (fox.cce.usp.br [143.107.70.1]) by bee08.uspnet.usp.br (8.6.8.1/RISC-CCE2.0) id UAA24134 Received: from localhost (szeinfel@localhost) by fox.cce.usp.br (8.6.4/CONVEX120-CCE2.0) id UAA24255 Date: Tue, 31 May 1994 20:31:56 -0300 (BDT) From: Rafael N Szeinfeld Subject: Re: CCL:HyperChem To: "Schriver, M;Chemistry;" cc: chemistry@ccl.net, mschriver@kean.ucs.mun.ca In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII He follows the answer not asking for a replay of the answers that I received. Hope that they are useful. Rafael Najmanovich ________________________List of Answers_________________________________ From slee@hyper.hyper.com Tue May 31 09:25:29 1994 Date: Mon, 30 May 1994 16:49:07 -0400 From: Thomas Slee To: Rafael N Szeinfeld Subject: Re: CCL:hyperchem. Dear Dr. Szeinfeld, If you have specific questions about HyperChem, please feel free to send them to info@hyper.com, and we'll do our best to provide you with answers to your questions. Alternatively, you may wish to join the HyperChem users' e-mail list where you can raise issues with many HyperChem users Should you wish to do this, send a message containing the single line subscribe hyperchem to hyperchem-request@hyper.com. The first widely available release of HyperChem became available just over two years ago, and usership has been growing steadily since then. There are not many papers published yet using HyperChem simply because of timing: at several months for the research and several more for the lad time for publication only those who started fast out of the blocks among our first customers have HyperChem-based material published. You do not say what area of chemical research you are interested in. We have customers pursuing research using HyperChem in many areas of chemistry and biochemistry, using the semi-empirical molecular orbital methods and molecular mechanics methods contained in the product. If you could be more specific about what kind of tasks you are looking to accomplish, I'd be happy to share what knowledge we have on HyperChem's capability in that area. Yours Tom Slee -- Tom Slee, Hypercube Inc., 419 Phillip St., Waterloo, Ont., Canada, N2L 3X2 E-Mail: slee@hyper.com, Tel. (519)725-4040, Fax. (519)725-5193. From TILBROOK@chem.surrey.ac.uk Tue May 31 09:25:43 1994 Date: 31 May 94 10:44:56 GMT From: Dave To: Rafael N Szeinfeld Subject: Re: CCL:hyperchem. Well Rafael, What HYPERCHEM seems to have its dveoteed beleivers and its out-right opponents. in concept it is good. But in reality it tries to do everything and doesn't do anything extremely well. If protein work is what you want to do and your systems aren't too big then perhaps it will meet you needs. Many people in our department have tried it out and have found that it is quite easy to get an answer out of it but extremely difficult to be sure how good that answer is - So caution! If you are into 'serious' computational chemistry then perhaps you should consider a tool specific to your needs. PC hyperchem does take a long time to do big calculations. We have run it on an SGI which is better but if you are going to invest large amounts in hardware then why not consider a system such as CERIUS or the BIO/POLYGRAF software from MSI? Of course this is just my opinion.... I'm sure others will disagree. Good Luck in your choice... you're the one who has to live with the software! Why not ask for an evaluation copy? Regards Dave Tilbrook ********************************************************** David Tilbrook * Tel: 44 483 300 800 x 2632 Polymer Group, * x 2617 Chemistry Department, * University of Surrey, * Fax: 44 483 300 803 Guildford, Surrey, GU2 5XH * U.K. * ********************************************************** From mn1@helix.nih.gov Tue May 31 20:42:56 1994 Received: from helix.nih.gov for mn1@helix.nih.gov by www.ccl.net (8.6.4/930601.1506) id UAA27371; Tue, 31 May 1994 20:04:00 -0400 Received: by helix.nih.gov (931110.SGI/1.35(big_sgi-1.0)) id AA15022; Tue, 31 May 94 20:04:00 -0400 Date: Tue, 31 May 94 20:04:00 -0400 From: mn1@helix.nih.gov (M. Nicklaus) Message-Id: <9406010004.AA15022@helix.nih.gov> To: CHEMISTRY@ccl.net Subject: Gauche effect ab initio calculations Cc: mn1@helix.nih.gov Dear Net-Workers, We are thinking about doing ab initio modeling (using Gaussian 92) on small organic molecules which possess, apart from C, H, N, O, a sulfur and a halogen atom (F, Cl, Br, I) in such an arrangement that we expect interactions of the gauche-effect type to occur between them. We would like to ask the experts what level of theory, basis sets, electron correlation methods etc. they would recommend for obtaining reliable conformational energies when calculating local energy minima for such compounds. Would different approaches be advisable for geometry optimization vs. the final energy calculation? Would using non-standard basis sets (which ones? obtainable where?) be necessary especially for the higher-period halogens? Please answer to me directly. I will summarize for the list if I get useful replies. Thanks in advance, Marc ------------------------------------------------------------------------ Marc C. Nicklaus Lab. of Medicinal Chemistry e-mail: mn1@helix.nih.gov National Cancer Institute, NIH Phone: (301) 402-3111 Bldg 37, Rm 5B29 Fax: (301) 496-5839 Bethesda, MD 20892 ------------------------------------------------------------------------ From C1790@SLVAXA.UMSL.EDU Tue May 31 21:42:53 1994 Received: from SLVAXA for C1790@SLVAXA.UMSL.EDU by www.ccl.net (8.6.4/930601.1506) id VAA27825; Tue, 31 May 1994 21:08:39 -0400 From: Received: from SLVAXA.UMSL.EDU by SLVAXA.UMSL.EDU (PMDF V4.2-11 #2503) id <01HD02F88NPCCWH6V8@SLVAXA.UMSL.EDU>; Tue, 31 May 1994 20:11:33 CST Date: Tue, 31 May 1994 20:11:33 -0600 (CST) Subject: QUESTION ABOUT X-DISPLAY SERVERS FOR PCs To: CHEMISTRY@ccl.net Message-id: <01HD02F89GMQCWH6V8@SLVAXA.UMSL.EDU> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT DEAR NETTERS, I'M LOOKING FOR FREE/CHEAP X-DISPLAY SERVER/CLIENT SOFTWARE FOR WINDOWS. I HEARD THAT 'EXCEED/W' FROM HUMMINGBIRD COMMUNICATIONS LTD., ONTARIO.CANADA, IS ONE POSSIBILITY. CAN SOMEONE GIVE ME THEIR PHONE NUMBER AND/OR ADDRESS? ARE THERE OTHER POSSIBILITIES OUT THERE THAT A NETTER CAN RECOMMEND? THANKS MUCH ... BILL WELSH DEPT. OF CHEMISTRY UNIV. OF MISSOURI-ST. LOUIS ST. LOUIS, MO 63121 From ostlund@hyper.hyper.com Tue May 31 22:42:52 1994 Received: from seraph.uunet.ca for ostlund@hyper.hyper.com by www.ccl.net (8.6.4/930601.1506) id WAA28664; Tue, 31 May 1994 22:23:31 -0400 Received: from hyper by mail.uunet.ca with UUCP id <119134-1>; Tue, 31 May 1994 22:23:14 -0400 Received: by hyper.hyper.com.hyper.com (931110.SGI/890607.SGI) (for ccl.net!chemistry) id AA25015; Tue, 31 May 94 22:28:05 -0400 Date: Tue, 31 May 1994 22:28:05 -0400 From: ostlund@hyper.hyper.com (Neil S. Ostlund) Message-Id: <9406010228.AA25015@hyper.hyper.com.hyper.com> To: chemistry@ccl.net Subject: HyperChem Reply! M. Schriver's recent posting implied that HyperChem might give semi-empirical results that are not to be trusted. I TAKE EXTREME EXCEPTION TO THIS INNUENDO! Hypercube Inc. includes quantum chemists who do know what they are doing. We have taken great pains to give the world an easy to use reliable version of semi-empirical technology. More QA (Quality Assurance) time has probably gone into HyperChem than any chemistry software package in history. HyperChem includes only published AM1 and PM3 parameters and reproduces the results of other programs in a commercial quality code that is easy to use and has been thoroughly tested. We have explicitly not generated any of our own parameters because our mandate with HyperChem is to make well-defined technology accessible and easy to use. If anyone from our thousands of users knows of a semi- empirical result from HyperChem that is inconsistent with published results, please let us know since we are unaware of any! Also, would the chemists who are "familiar with theoretical chemistry" and are trashing HyperChem please stand up and be counted. I will stake what scientific reputation I have, including a name on the first paper in the literature (almost thirty years ago!) that described the INDO method, the basis of almost all of these semi-empirical methods, on HyperChem. I also offer an autographed copy of Szabo and Ostlund, "Modern Quantum Chemistry", to the first person to report a legitimate error in the semi-empirical results coming from HyperChem. Hypercube Inc. people, who have always had sole responsibility for the HyperChem product development, includes five respected and experienced Ph.D. quantum chemists. We stand by our products. ------------ Neil Ostlund President, Hypercube Inc. 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: ostlund@hyper.com