From PHTH1@cc.newcastle.edu.au Mon Jul 25 01:56:13 1994 Received: from BROLGA.NEWCASTLE.EDU.AU for PHTH1@cc.newcastle.edu.au by www.ccl.net (8.6.9/930601.1506) id AAA28910; Mon, 25 Jul 1994 00:57:33 -0400 Received: from cc.newcastle.edu.au by cc.newcastle.edu.au (PMDF V4.3-8 #6545) id <01HF4L8JTKCW9APAPV@cc.newcastle.edu.au>; Mon, 25 Jul 1994 14:57:34 +1000 Date: Mon, 25 Jul 1994 14:54:26 +1000 From: Tony Dyson Subject: CAMP-ATAMI Manual Translation To: chemistry@ccl.net Message-id: <01HF4LGZIZR49APAPV@cc.newcastle.edu.au> MIME-version: 1.0 Content-transfer-encoding: 7BIT I have available an English translation of part of the CAMP-ATAMI manual. It is Chapters 3 & 4, which describe the input and output of the program respectively. I have the translated chapters in three formats: WP5.1, postscript and rtf. I would be happy to mail a copy to anybody who would like one. If the JCPE or CAMP-ATAMI people wish to make available a central location for these to be retrieved from, I would also be happy to upload the three files. Tony --------------------------------------------------------------------- Anthony J. Dyson Surface Theory Group Dept. of Physics, University of Newcastle Australia phth1@cc.newcastle.edu.au --------------------------------------------------------------------- From toukie@zui.unizh.ch Mon Jul 25 04:56:31 1994 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.9/930601.1506) id EAA00227; Mon, 25 Jul 1994 04:50:05 -0400 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA21734; Mon, 25 Jul 94 10:50:58 +0200 X-Nupop-Charset: British Date: Mon, 25 Jul 1994 09:47:16 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <35252.toukie@zui.unizh.ch> To: chemistry@ccl.net Subject: Calculations for hydrogen isotopes Dear Colleagues, Does anyone know of programmes that can (i) calculate bond strengths/ bond lengths of carbon-protium, carbon-deuterium, and carbon-tritium in alkyl (sp3) molecules? (ii) calculate the rotation energy barriers for chiral methyl groups CHDT attached to unhindered alkyl moieties relative to that for CH3? Thanks to all responders in advance. Sincerely, S. Shapiro Institut fuer orale Mikrobiologie Zentrum fuer Zahn-, Mund- und Kieferheilkunde der Universitaet Zuerich Plattenstrasse 11 Postfach CH-8028 Zuerich, Switzerland Internet: toukie@zui.unizh.ch From fdeprof@is1.vub.ac.be Mon Jul 25 05:56:16 1994 Received: from rc1.vub.ac.be for fdeprof@is1.vub.ac.be by www.ccl.net (8.6.9/930601.1506) id FAA00518; Mon, 25 Jul 1994 05:42:51 -0400 Received: from is1e.vub.ac.be by rc1.vub.ac.be (8.6.8.1/2.23.ap) id LAA08223; Mon, 25 Jul 1994 11:44:37 +0200 Received: from sterfpmc211.vub.ac.be by is1e.vub.ac.be (5.61/BFUCC-920211) id AA23925; Mon, 25 Jul 94 11:43:46 +0200 Date: Mon, 25 Jul 94 11:43:46 +0200 Message-Id: <9407250943.AA23925@is1e.vub.ac.be> X-Sender: fdeprof@is1.vub.ac.be (Unverified) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: fdeprof@is1.vub.ac.be Subject: Integrating electron densities Hello, Does anyone know of any programs integrating atomic electron densities numerically starting from a grid of points ? Thanks From h.rzepa@ic.ac.uk Mon Jul 25 05:57:19 1994 Received: from judy.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.9/930601.1506) id FAA00530; Mon, 25 Jul 1994 05:44:21 -0400 Received: from sg1.cc.ic.ac.uk by judy.ic.ac.uk with SMTP (PP) id <23920-0@judy.ic.ac.uk>; Mon, 25 Jul 1994 10:44:28 +0100 Received: from macb.ch by cscmgb.cc.ic.ac.uk (920330.SGI/4.0) id AA26052; Mon, 25 Jul 94 10:46:38 +0100 Message-Id: <9407250946.AA26052@cscmgb.cc.ic.ac.uk> X-Sender: rzepa@sg1.cc.ic.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 25 Jul 1994 10:44:28 +0100 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Rzepa,Henry) (Rzepa,Henry) Subject: Re: Chemical MIME and Internet discussion An update to the Hyperactive Molecules page. We now have 16 examples of hyperactive molecules, but are looking for more. If anyone knows of other examples, please let me know. We are also interested in applications in other areas, such as NMR, dynamics, neural networks etc. If anyone has a URL describing a conference, workshop or invited talk in any area of chemistry, you can submit it to a "talks" page via a forms interface; http://www.ch.ic.ac.uk/talks/ Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 2.02, Tel (44) 171 594 5774 or 594 5809. Fax: (44) 171 594 5804 World-Wide-Web URL: http://www.ch.ic.ac.uk/rzepa.html From chp1aa@surrey.ac.uk Mon Jul 25 10:56:22 1994 Received: from mail-server.surrey.ac.uk for chp1aa@surrey.ac.uk by www.ccl.net (8.6.9/930601.1506) id KAA03313; Mon, 25 Jul 1994 10:47:44 -0400 Received: from central.surrey.ac.uk by mail-server.surrey.ac.uk with SMTP using (PP) id <12070-0@mail-server.surrey.ac.uk>; Mon, 25 Jul 1994 15:26:10 +0100 Received: by central.surrey.ac.uk (1.37.109.8/16.2) id AA17462; Mon, 25 Jul 1994 15:26:07 +0100 From: Mr Andrew D Allen Message-Id: <9407251426.AA17462@central.surrey.ac.uk> Subject: CCL: ClustAnal: Summary. To: chemistry@ccl.net Date: Mon, 25 Jul 94 15:26:06 BST Mailer: Elm [revision: 70.85] I have uploaded a copy of all messages recieved as regards my search for a cluster analysis program. Since my stats knowledge is limited it will take me some time to digest the information from some of these replies but in the mean time help yourselves. download from 131.227.110.69 {ftp : anonymous} /pub/Cluster_Analysis/CA_SUM I hope to post a summary to the net once i've been able to go through the available stats packages. Andy -- ############################################################################### Structural and Computation Chemistry Group_________chp1aa@uk.ac.surrey - JANET. Department of Chemistry____________________________phone_______+44(483)-259591. University of Surrey_______________________________fax_________+44(483)-300803. Guildford, Surrey, GU2 5XH, UK_____________________ftp____________131.227.110.2 ############################################################################### From MOSES@cmchem.chem.cmu.edu Mon Jul 25 11:00:05 1994 Received: from cmchem.chem.cmu.edu for MOSES@cmchem.chem.cmu.edu by www.ccl.net (8.6.9/930601.1506) id KAA03012; Mon, 25 Jul 1994 10:21:08 -0400 Date: Mon, 25 Jul 1994 10:22:44 -0400 (EDT) From: "D.J. Moses, 412-279-6700, 412-279-2118 (Fax)" To: chemistry@ccl.net CC: MOSES@cmchem.chem.cmu.edu Message-Id: <940725102244.20201da9@cmchem.chem.cmu.edu> Subject: Gaussian Workshop at NESC **************************************************************************** NESC announces: INTRODUCTION TO GAUSSIAN: THEORY AND PRACTICE Date: September 21-23, 1994 Location: National Environmental Supercomputing Center (NESC) Bay City, Michigan The NESC is pleased to offer "Introduction to Gaussian: Theory and Practice." This workshop will be presented in conjunction with Gaussian, Inc., on September 21-23, 1994 at the National Environmental Supercomputing Center of the EPA in Bay City, MI. The workshop is intended to offer an overview of the Gaussian package which could act as an introduction to electronic structure methods or as a review for researchers active in the field. The workshop is open to researchers at all levels of academic, government and industrial research. Gaussian 92 is a user-friendly set of programs for performing ab initio and semi-empirical molecular orbital calculations. This workshop provides an introduction to the underlying theory along with practical pointers. All of the ab initio methods available in Gaussian 92/DFT will be covered, along with discussion on choosing methods appropriate to the chemistry being studied. Additional topics will include estimating computer resource requirements and dealing with computational difficulties. Instructors: Dr. Michael J. Frisch Lorentzian, Inc. Prof. H. Bernard Schlegel Wayne State University Dr. Douglas J. Fox Gaussian, Inc. Dr. Krish Namboodiri Martin Marietta/NESC Tentative Agenda Topics: Building Gaussian Input Decks Model Chemistries (basis sets, level of theory) SCF Methods (RHF/UHF/ROHF, GVB, MCSCF) Geometry Optimization Techniques Electron Correlation Methods Density Functional Theory Methods Excited States via CI Singlets Interpretation of Results and Molecular Properties Solvent Effects on Molecular Electronic Structure Gaussian Utilities Performance of Model Chemistries There will be hands-on sessions each day between the morning and afternoon lectures. Additional hands-on sessions will be available until the building closes. Workshop participants will be provided with a class computer account, of limited allocation, on the NESC Cray and a workstation for use during the hands-on workshop sessions. Each workshop participant will also be provided a copy of the lecture notes, a copy of the Gaussian 92 User's Guide, and a copy of "Exploring Chemistry with Electronic Structure Methods: A Guide to Using Gaussian." ---------------------------------------------------------------------------- APPLICATION PROCEDURE All applicants must submit the attached application form and a cover letter which briefly (one or two paragraphs) describes your current research and how participating in this workshop will enhance your research. The cover letter should also include one or two sentences indicating your level of experience with computers. Seats are limited and the potential applicants are encouraged to send the application material ASAP. There is no course fee for this workshop but participants are responsible for all travel, lodging and meals. Hotel and travel accommodation selections will be mailed to conference participants in due course. PLEASE RETURN YOUR APPLICATION MATERIALS TO: Dr. Krish Namboodiri Martin Marietta/NESC 135 Washington Ave. Bay City, MI 48708 - 5845 For more information, please contact Dr. Namboodiri at the NESC: Telephone:(517) 894-7600 Fax: (517)894-7676 Email: nke@spruce.nesc.epa.gov DEADLINES: Receipt of Registration Materials: August 15, 1994 ---------------------------------------------------------------------------- APPLICATION FORM: Name: Affiliation: Address: Telephone: Facsimile: E-Mail Address: Nationality: Passport Number (for noncitizens): Are you a current NESC systems user? Machine and User Account Name: Please indicate your Research Standing (check one): Faculty _______ Postdoctorate _______ Graduate Student ______ Undergraduate Student _______ University Research Staff _______ University Non-Research Staff ______ Government _______ Industrial ______ Other ______ Remember to include the cover letter with the additional information. ---------------------------------------------------------------------------- GAUSSIAN, INC. Carnegie Office Park Building 6 Pittsburgh, PA 15106 USA PHONE - 412-279-6700 FAX - 412-279-2118 E-MAIL - info@gaussian.com ---------------------------------------------------------------------------- This notice is sent without warranty of any kind, express or implied by Gaussian, Inc. or the EPA. Gaussian and Gaussian 92 are registered trademarks of Gaussian, Inc. **************************************************************************** From stevens@rainbow.uchicago.edu Mon Jul 25 11:56:57 1994 Received: from midway.uchicago.edu for stevens@rainbow.uchicago.edu by www.ccl.net (8.6.9/930601.1506) id LAA03554; Mon, 25 Jul 1994 11:02:53 -0400 Received: from rainbow.uchicago.edu by midway.uchicago.edu for CHEMISTRY@ccl.net Mon, 25 Jul 94 10:03:37 CDT Received: by rainbow.uchicago.edu (920330.SGI/920502.SGI) for @midway.uchicago.edu:CHEMISTRY@ccl.net id AA18221; Mon, 25 Jul 94 10:38:58 -0500 From: stevens@rainbow.uchicago.edu (Jonathan Stevens) Message-Id: <9407251538.AA18221@rainbow.uchicago.edu> Subject: Geometry optimizations (summary of replies) To: CHEMISTRY@ccl.net Date: Mon, 25 Jul 1994 10:38:58 -0600 (CDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 7559 Hello, Recently I posted a request for a text or review article detailing the methods of ab initio geometry optimizations. Appended is a summary of the replies I received. Thanks to all respondents. Jonathan E. Stevens From Patrick.Bultinck@rug.ac.be Tue Jul 19 07:03:58 1994 Received: from [157.193.40.37] by rainbow.uchicago.edu via SMTP (920330.SGI/920502.SGI) for stevens id AA07160; Tue, 19 Jul 94 07:03:58 -0500 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA10182 (5.67b/IDA-1.5 for ); Tue, 19 Jul 1994 13:45:15 +0200 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA10005; Tue, 19 Jul 94 13:42:04 +0200 Date: Tue, 19 Jul 1994 13:42:04 +0200 (MET DST) From: Patrick Bultinck Subject: Re: CCL:geometry optimizations To: Jonathan Stevens In-Reply-To: <9407181341.AA00626@rainbow.uchicago.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 846 Status: RO On Mon, 18 Jul 1994, Jonathan Stevens wrote: > > > hello, > > i am interested to know if there is a good text, or review article, > explaining and detailing the various techniques of ab initio molecular geometry > optimizations. > Thank you in advance, > Jonathan E. Stevens > > > Have a look at : Schlegel, Adv. in Chem. Phys., ab initio methods in quantum chemistry, Vol. LXVII, 1987, part I, pp 249-285 It is a nice article with a lot of literature references, so you can find your way through a lot of literature. In part II you can find an article by Pulay that will give you some interesting things on the analytical derivative methods in Quantum Chemistry. Methods that are among those used in optim. greetings, Patrick, University of Ghent, Belgium From chemistry-request@ccl.net Mon Jul 18 15:18:23 1994 Received: from www.ccl.net by rainbow.uchicago.edu via SMTP (920330.SGI/920502.SGI) for stevens id AA23670; Mon, 18 Jul 94 15:18:23 -0500 Received: for chemistry-request@ccl.net by www.ccl.net (8.6.9/930601.1506) id PAA04057; Mon, 18 Jul 1994 15:00:12 -0400 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.9/930601.1506) id OAA01330; Mon, 18 Jul 1994 14:17:21 -0400 Received: from localhost (elewars@localhost) by alchemy.chem.utoronto.ca (8.6.4/8.6.4) id OAA22654 for chemistry@ccl.net; Mon, 18 Jul 1994 14:17:24 -0400 Date: Mon, 18 Jul 1994 14:17:24 -0400 From: "E. Lewars" Message-Id: <199407181817.OAA22654@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: CCL:Books that show how to do ab in optimizations Sender: chemistry-request@ccl.net Errors-To: ccl@ccl.net Precedence: bulk Status: RO Jonathon Stevens asks about books that tell you how to do ab in opt's. Some recent books are A Spartan Tutoria, W. J. Hehre, L. D. Burke, and A. J. Shusterman This is supplied with the Spartan MM/Semiemp/Ab In computational program. If you don't have Spartan (so much the worse for you), you may still find the tutorial helpful with other programs. Practical Strategies for Electronic Structure Calculations, W. J. Hehre, L. D. Burke Evaluation of Modern Electronic Structure Methods, W. J. Hehre Experiments in Computational Organic Chemistry W. J. Hehre, L. D. Burke, A. J. Shusterman and W. J. Pietro All four are published by Wavefunction, Inc, 18401 Von Karman Ave Suite 370, Irvine CA 92715 (714)955-2120, FAX (714)955-2118) They are oriented toward the use of the highly graphical Spartan program of Wavefunction. Another useful book, designed for instruction in the Gaussian programs (G92 in particular) is Exploring Chemistry with Electronic Structure Methods, by James B. Foresman and Aeleen Frisch, available from Gaussian Inc., 4415 Fifth Ave, Pittsburgh, PA 15213, (412)279-6700, FAX ....-2118; info@gaussian.com All these books apeared in the last year or two. ==== Errol Lewars === ---Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV From fournie@ned1.sims.nrc.ca Mon Jul 18 11:07:22 1994 Received: from ned1.sims.nrc.ca by rainbow.uchicago.edu via SMTP (920330.SGI/920502.SGI) for stevens id AA04211; Mon, 18 Jul 94 11:07:22 -0500 Message-Id: <9407181552.AA25331@ned1.sims.nrc.ca> From: fournie@ned1.sims.nrc.ca (Dr. Rene Fournier) Subject: Geometry optimization To: stevens Date: Mon, 18 Jul 94 11:52:27 EDT X-Mailer: ELM [version 2.3 PL11] Status: RO Hello ; I recommend the very good review article "Optimization of equilibrium geometries and transition structures" by H. B. Schlegel, Advances in Chemical Physics 67 (1987) pp. 249-286. Then, if you are interested in developments since 1987, here are some interesting papers: 1. Partial optimization of large molecules and clusters, J. D. Head, J. Comput. Chem. 11 (1990) 67. 2. Geometry optimization in cartesian coordinates: constrained optimization, J. Baker, J. Comput. Chem. 13 (1992) 240. 3. Algorithmic tools in the study of semiempirical potential surfaces, D. A. Liotard, Int. J. Quantum Chem. 44 (1992) 723. 4. Geometry optimization in redundant internal coordinates, P. Pulay and G. Fogarasi, J. Chem. Phys. 96 (1992) 2856. Rene Fournier fournie@ned1.sims.nrc.ca Steacie Institute for Molecular Sciences, NRC, Ottawa. (613) 990 0964 From ferenc@rchsg8.chemie.uni-regensburg.de Mon Jul 18 10:39:59 1994 Received: from comsun.rz.uni-regensburg.de by rainbow.uchicago.edu via SMTP (920330.SGI/920502.SGI) for stevens id AA03127; Mon, 18 Jul 94 10:39:59 -0500 Received: from rchsg8.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA01121 (5.65c/IDA-1.4.4 for ); Mon, 18 Jul 1994 17:25:05 +0200 Received: by rchsg8.chemie.uni-regensburg.de (931110.SGI/URRZ-Sub-1.5-irix) (for stevens@rainbow.uchicago.edu) id AA21920; Mon, 18 Jul 94 17:23:03 +0200 Date: Mon, 18 Jul 94 17:23:03 +0200 From: Ferenc.Molnar@chemie.uni-regensburg.de (Ferenc Molnar) Message-Id: <9407181523.AA21920@rchsg8.chemie.uni-regensburg.de> To: stevens (Jonathan Stevens) Subject: Re: CCL:geometry optimizations Status: RO Hi, try the Appendix C of "Modern Quantum Chemistry", by Szabo, A., and Ostlund, N.S., McGraw-Hill. Best regards, Ferenc Ferenc Molnar --------------------------------------------------------------------------- Institut fuer Physikalische und Theoretische Chemie - Lehrstuhl Prof. Dick - Tel.: (+49) 941 943-4466 /-4486 Universitaet Regensburg Fax.: (+49) 941 943-4488 Universitaetsstrasse 31 D-93053 Regensburg Deutschland / Germany --------------------------------------------------------------------------- EMail (SMTP): Ferenc.Molnar@chemie.uni-regensburg.de --------------------------------------------------------------------------- :-) I wish to have no connection with any ship that does not sail fast, for I intend to go in harm's way. -- John Paul Jones, USN 1747-1792 ;-) --------------------------------------------------------------------------- From FS300627@Sol.YorkU.CA Mon Jul 25 12:56:25 1994 Received: from Sol.YorkU.CA for FS300627@Sol.YorkU.CA by www.ccl.net (8.6.9/930601.1506) id MAA05373; Mon, 25 Jul 1994 12:29:42 -0400 From: Received: from Sol.YorkU.CA by Sol.YorkU.CA (PMDF #12410) id <01HF4GBC473K8Y82KP@Sol.YorkU.CA>; Mon, 25 Jul 1994 12:29 EDT Date: Mon, 25 Jul 1994 12:29 EDT Subject: IN-house modelling To: chemistry@ccl.net Message-id: <01HF4GBC473K8Y82KP@Sol.YorkU.CA> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" Greetings, I remember that a couple of weeks ago someone posted a question about in-house vs out-house molecular modelling. I would like to obtain the summery about that if possible. Thanks in advance Patrick M. van der Valk, M.Sc. BioMimic Toronto From jlchen@scripps.edu Mon Jul 25 13:56:22 1994 Received: from scripps.edu for jlchen@scripps.edu by www.ccl.net (8.6.9/930601.1506) id NAA06208; Mon, 25 Jul 1994 13:27:13 -0400 Received: from maxwell.scripps.edu by scripps.edu (5.61/1.34) id AA22515; Mon, 25 Jul 94 10:28:03 -0700 Received: by maxwell.Scripps.EDU (4.1/SMI-4.1/TSRI1.0) id AA00692; Mon, 25 Jul 94 10:31:57 PDT Date: Mon, 25 Jul 1994 10:28:33 -0700 (PDT) From: Jun Liang Chen Subject: Re: CCL:CAMP-ATAMI Manual Translation To: Tony Dyson Cc: chemistry@ccl.net In-Reply-To: <01HF4LGZIZR49APAPV@cc.newcastle.edu.au> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 25 Jul 1994, Tony Dyson wrote: > > I have available an English translation of part of the CAMP-ATAMI > manual. It is Chapters 3 & 4, which describe the input and output > of the program respectively. > > I have the translated chapters in three formats: WP5.1, postscript > and rtf. I would be happy to mail a copy to anybody who would like > one. If the JCPE or CAMP-ATAMI people wish to make available a > central location for these to be retrieved from, I would also be > happy to upload the three files. > Dear Dr. Dyson, If possible, I would like to have the translated chapters in postscript form via e-mail. Tnanks! jlchen From srheller@asrr.arsusda.gov Mon Jul 25 14:56:23 1994 Received: from asrr.arsusda.gov for srheller@asrr.arsusda.gov by www.ccl.net (8.6.9/930601.1506) id OAA07192; Mon, 25 Jul 1994 14:40:52 -0400 Message-Id: <199407251840.OAA07192@www.ccl.net> Date: 25 Jul 94 14:30:00 EDT From: "STEPHEN R. HELLER" Subject: Software/Databases for Review To: "chemed-l" cc: "chminf-l" , "chemistry" , "orgchem" 25 July, 1994 Subject: Computer Software for Review As the Software Review Editor for the ACS Journal of Chemical Information and Computer Science (JCICS) I often get software for review in the journal. I now have twelve packages in hand (see below) and I am looking for someone who is willing to review these software/databases products. In return for the review you get to keep the software. The review should be completed in 1-3 months. The length of the review is 4-10 double spaced typed pages. Sample reviews can be found in most of the recent issues of JCICS. Please try to give me some (short) reason to choose you over another person. DO NOT SAY YOU WILL REVIEW ANYTHING I HAVE AVAILABLE. Messages with such replies are trashed! I have tried this approach for about the past three years and it is working reasonably well. (REMINDER: For those who haven't finished your reviews of software sent months and months ago, this last sentence does not apply to you!) As a result, I am continuing this new method to find reviewers using this e- mail/user group system. I reserve the right to abandon this if it is a problem, or inappropriate. I will not notify people if I have found a reviewer. If you don't hear from me within a few days I have chosen someone else to review the particular package. As I get many, many, (too many) replies to this message, please do not respond after 27 July, 1994 (Wednesday), as I am sure the software will be gone by then. I can be reached on Internet (SRHELLER@ASRR.ARSUSDA.GOV). PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE, and FAX NUMBER!!! (I send the software by Federal Express.) Without this information I WILL NOT consider your request. Steve Heller The packages I now have are: 1. Accord for Excel (4.0 and 5.0) from Synopsys Ltd (Leeds, UK) allows one to manage chemistry and associated data within Excel. For the IBM PC. Does NOT include the Microsoft Excel software! (The following softwre packages are from SYRACUSE RESEARCH). 2. LOGKOW This program estimates the log octanol-water partition coefficient (log P) of organic chemicals using an atom/fragment contribution method developed at SRC (Group Contribution Method for Estimating Octanol/Water Partition Coefficients, SETAC Meeting in Cincinnati, OH, Nov 1992;updated manuscript submitted to J. Pharmac. Sci.). Chemical structures are entered using SMILES notation [butanol = CCCCO, J Chem Inf Comput Sci 28: 31-36 (1988). Using a training set of 2351 chemicals with 125 groups and 230 correction factors, a correlation coefficient (r2) of 0.98 was found between the experimental and estimate log Kow's. The method was evaluated using a validation set of experimental values for 6055 chemicals other than those included in the training set with a resulting r2 of 0.94 and a mean error of 0.31. Both PC compatable DOS and Windows 3.1 or higher versions are available for this and all of the following programs. 3. DERMAL This program estimates the dermal permeability coefficient (Kp) and the dermally absorbed dose per event (DAevent) of organic compounds using chemical structure input and the above program to estimate the octanol/water partition coefficient. The estimation methodology was taken from the U.S. EPA document Dermal Exposure Assessment: Principles and Applications (EPA/600/8-91-011B, January 1992). The program uses one general estimation equation and three specific class estimation equations to predict Kp. DAevent is predicted by two separate methods (an adapted equation of Fick's first law and another method both of which are indicated in the EPA report) and requires (1) input of the duration of the event, and (2) concentration of the chemical in water (a default water solubility is calculated for the user if no value is entered). 4. Atmospheric Oxidation Rate Program This program estimates the gas-phase reaction rate between organic chemicals and hydroxyl radicals using the estimation methods developed by Dr. Roger Atkinson and co-workers [Internat J Chem Kinetics 19: 799-828 (1987); Chem Rev 85: 69-201 (1985); Environ Toxicol Chem 7: 435-442 (1988)]. Ozone reaction rates are also estimated for olefinic and acetylenic compounds [Chem Rev 84: 437-470 (1984)]. Chemical structures are entered using SMILES notation and available experimental values for reaction rates with hydroxyl radicals, ozone, and nitrate radicals are presented. The hydroxyl radical and ozone rate constants are calculated using the Atkinson method and the atmospheric half-life is also estimated using an average hydroxyl radical concentration and an average ozone concentration. See Chemosphere 26:2293-2299 (1993) 5. Henry's Law Constant Program This program calculates the Henry's Law constant (air/water partition coefficient) from SMILES notation structure using both the group contribution and the bond contribution method of Hine and Mookerjee [J Org Chem 40: 292-8 (1975)]. SRC has recently published a paper describing the correlations [Environ Toxicol Chem 10:1283-93 (1991)] and has updated the group contribution coefficients with new experimental data. 6. Biodegradation Probability Program. This program calculates the probability that a chemical under aerobic conditions with mixed cultures of microorganisms will biodegrade rapidly or slowly. It uses fragment constants developed using multiple linear and non-linear regressions and data from SRC's data base of evaluation biodegradation data (BIODEG file). The results have been published [Environ Toxic Chem 11:593-603 (1992)]. A new version of the program is now available that uses the previous experimental data and some new expert survey data. The model uses a slight revision of the previous fragments and molecular weight to (a) calculate the probability of rapid biodegradation from the experimental data, and (b) to estimate the primary and ultimate biodegradation times for complete degradation (days, weeks, months, longer) using the evaluations of 200 chemicals by 17 biodegradation experts [Environ. Sci. & Technol 28: 459-465 (1994)]. 7. PC-HYDRO. This program calculates the hydrolysis rate constant for esters, carbamates, halomethanes, alkyl halides, and epoxides using a method developed by the U.S. EPA's Office of Pollution Prevention and Toxics. It uses SMILES notation structural input to calculate a second-order acid- or base-catalyzed hydrolysis rate constant at 25o C. Acid- and base-catalyzed half-lives are calculated for pH 7 and/or pH 8. 8. PC-KOC This program calculates the soil or sediment adsorption coefficient (Koc) (ratio of the chemical adsorbed per unit weight of organic carbon (oc) in the soil or sediment to the concentration of the chemical in solution at equilibrium). SMILES notation structural input are used to calculate the Koc from a correlation to the molecular connectivity indices and correction factors for certain chemical classes. The method was developed with the U.S. EPA's Office of Pollution Prevention and Toxics using a training set of 189 chemicals and evaluated with a validation set of 131 chemicals. R2 for the validation set was 0.92. The results have been published [Environ Sci. Technol. 26:1560-67 (1992)]. 9. ChemBase Physical Properties Data Base Contains chemical structures and names (approximately 7,000) and physical properties (melting point, boiling point, water solubility, vapor pressure, dissociation constant, octanol/water partition coefficient, and Henry's Law constant) for over most of the chemicals. With this Physical Properties Data Base and the ChemBase software, one can substructure search, name fragment search, or search by physical properties. This is an excellent starter data base for new ChemBase , ISIS Base , or MACCS users who need a base set of chemical structures and physical properties. 10. PC Environmental Fate Data Bases SRC's Environmental Fate Data Bases is available in a PC version for IBM compatibles with similar software to that available on the VAX version. Each of the four major files (DATALOG , CHEMFATE , BIOLOG , and BIODEG ) are available separately and include the corresponding full references from the 23,000 references in the full citation file, XREF (requires 14 Mb for support files and software). These are each briefly discussed below. DATALOG This file is the largest, containing about 218,000 records on about 13,800 chemicals. This file indicates where environmental fate and exposure data can be found by using 18 different indexing terms (e.g., water solubility, Henry's Law constant, hydrolysis, and ambient monitoring). Requires additional 13 Mb. CHEMFATE This file contains actual physical property values, rate constants, and monitoring concentrations for approximately 1700 commercially significant chemicals. Recently, recommended physical property values were collected for the SARA Section 313 TRI chemicals. Requires additional 26 Mb. BIOLOG This file, which contains about 45,000 records, indicates sources of microbial toxicity and biodegradation data on approximately 6500 chemicals. Indexing and searching is allowed on toxicity or biodegradation data; aerobic or anaerobic conditions; pure enzyme, cell free extract, pure culture, or mixed culture; source of microorganisms (e.g., soil, sewage, etc.); and whether the metabolism pathway has been studied. (2.6 Mb). BIODEG This file contains actual experimental results on biodegradation studies for approximately 700 chemicals. Experimental details, such as chemical concentration and rate of degradation, are included. This file was used to develop the Biodegradation Probability Program. (13 Mb). 11. Chapman & Hall CD-ROM of the Dictionary of Drugs. 12. Chapman & Hall CD-ROM of the Dictionary of Analytical Reagents. From MARLA@chemf.rutgers.edu Mon Jul 25 15:56:29 1994 Received: from chemf.rutgers.edu for MARLA@chemf.rutgers.edu by www.ccl.net (8.6.9/930601.1506) id PAA07856; Mon, 25 Jul 1994 15:16:29 -0400 Date: Mon, 25 Jul 94 14:18 EST From: Marla Babcock Subject: CCL:Meeting in Brazil? To: chemistry@ccl.net Message-id: X-Organization: Department of Chemistry at Rutgers University X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" I remember reading something about a meeting in Brazil next year for modeling. Does anyone know anything about it? I have a friend who would like to know more. Thanks in advance Marla Babcock From SATYAM@vms.cis.pitt.edu Mon Jul 25 15:57:24 1994 Received: from VM2.CIS.PITT.EDU for SATYAM@vms.cis.pitt.edu by www.ccl.net (8.6.9/930601.1506) id PAA08250; Mon, 25 Jul 1994 15:43:03 -0400 From: Received: from vms.cis.pitt.edu by vms.cis.pitt.edu (PMDF V4.2-14 #4065) id <01HF4MXYLGXS98DTL9@vms.cis.pitt.edu>; Mon, 25 Jul 1994 15:43:48 EST Date: Mon, 25 Jul 1994 15:43:47 -0500 (EST) Subject: READING PDB FILE ... IN ICON8 (EXTENDED HUCKEL) program To: chemistry@ccl.net Message-id: <01HF4MXYLQKY98DTL9@vms.cis.pitt.edu> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT dear netters, Anyone with experience for modifying Icon8 (extended huckel) code for reading pdb file and keeping track of basis fns..in the order of pdb file rather than icon-input-format. Thanks in advance for suggestions. Satyam From friedman@tammy.harvard.edu Mon Jul 25 15:58:09 1994 Received: from tammy.harvard.edu for friedman@tammy.harvard.edu by www.ccl.net (8.6.9/930601.1506) id PAA07906; Mon, 25 Jul 1994 15:21:55 -0400 Received: by tammy.harvard.edu (5.64/10.0) id AA04570; Mon, 25 Jul 94 15:23:45 -0400 Date: Mon, 25 Jul 94 15:23:45 -0400 From: friedman@tammy.harvard.edu (Dawn Friedman) Message-Id: <9407251923.AA04570@tammy.harvard.edu> To: chemistry@ccl.net Subject: in-house modelling summary I've (finally) sent out that summary to those who requested it. If you don't receive yours within a reasonable time, please email me and I'll send it again. I've had a few copies returned by various mailer-daemons already. FS300627@Sol.YorkU.CA, your copy is on its way. Thanks for all your help with this rather hot topic, --Dawn friedman@tammy.harvard.edu From DSMITH@uoft02.utoledo.edu Mon Jul 25 15:59:04 1994 Received: from uoft02.utoledo.edu for DSMITH@uoft02.utoledo.edu by www.ccl.net (8.6.9/930601.1506) id PAA08087; Mon, 25 Jul 1994 15:32:48 -0400 Received: from UOFT02.UTOLEDO.EDU by UOFT02.UTOLEDO.EDU (PMDF V4.3-7 #5345) id <01HF4L6HC90W0003G3@UOFT02.UTOLEDO.EDU>; Mon, 25 Jul 1994 15:32:57 EST Date: Mon, 25 Jul 1994 15:32:57 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: COMP elections - please send ballots now To: chemistry@ccl.net, hyperchem@autodesk.com, mmodinfo@uoft02.utoledo.edu Message-id: <01HF4L6HE4JM0003G3@UOFT02.UTOLEDO.EDU> X-Envelope-to: chemistry@ccl.net X-VMS-To: CHEMISTRY, HYPERCHEM, MMODINFO MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT SECOND NOTICE The Computers in Chemistry Division (COMP) of the American Chemical Society is in the process of collecting ballots for next year's Chairman-elect and Councilor. Ballots were included in the COMP News, the division newsletter. RESPONSE HAS BEEN POOR AND MANY MORE BALLOTS ARE NEEDED! VOTE NOW! The nominees for Chairman-elect are: Frank K. Brown and Christopher J. Cramer The nominees for Councelor are: Randall L. Cain, Philip D. Kutzenco and Goerge W. A. Milne If you are a member of the division and do not have your ballot or access to a copy of COMP News, you may request a ballot by sending me your fax number. Alternatively, you may simply write your choices (vote for one person for each office) on a piece of paper and send them to: Dr. M. Katharine Holloway Merck Research Labs P.O. Box 4 West Point, PA 19486 Douglas A. Smith voice: (419)537-2116 Associate Professor fax: (419)537-4033 Department of Chemistry email: dsmith@uoft02.utoledo.edu and Center for Drug Design and Development and Chairman-elect ACS Division of Computers in Chemistry The University of Toledo Toledo, OH 43606-3390 From raeker@tc6.fi.ameslab.gov Mon Jul 25 16:01:10 1994 Received: from tc6.fi.ameslab.gov for raeker@tc6.fi.ameslab.gov by www.ccl.net (8.6.9/930601.1506) id PAA08163; Mon, 25 Jul 1994 15:39:34 -0400 Received: by tc6.fi.ameslab.gov (920330.SGI/921111.SGI.AUTO) for chemistry@ccl.net id AA04901; Mon, 25 Jul 94 14:39:07 -0500 From: raeker@tc6.fi.ameslab.gov (Todd J. Raeker) Message-Id: <9407251939.AA04901@tc6.fi.ameslab.gov> Subject: no subject (file transmission) To: chemistry@ccl.net Date: Mon, 25 Jul 1994 14:39:02 -0600 (CDT) X-Mailer: ELM [version 2.4 PL5] Content-Type: text Content-Length: 1653 I will be purchasing at least 2 high performance workstations in the very near future and am soliciting advice from real users rather the salespersons hype. I will be doing MD simulations of systems containing about 15,000-20,000 atoms and need the fastest machine I can get that is reasonable priced. I have looked at the new IBM RS/6000 380 & 390 models and am very impressed with the specs. Since these are new models, I suspect not many people on this list have one but if anyone has, I would be interested in any experience you may have had so far. Also, I would like to hear from people who have workstations that have SPECfp92 ratings of about 150 or greater. As I write this I realize that most likely these types of questions come up periodically. Being that most people on this list are ussually involved in similiar searchs, it might be a good idea to maintain some sort of FAQ summarizing the real life performance of workstations. If there is any interest and one does not already exist, I will volunteer to maintain such a file that would be available via ftp. Let me know what you think. Regards. Todd From hou@agouron.com Mon Jul 25 17:56:37 1994 Received: from agouron.com for hou@agouron.com by www.ccl.net (8.6.9/930601.1506) id RAA09442; Mon, 25 Jul 1994 17:29:45 -0400 Received: from agouron.agouron.com by agouron.com via SMTP (940406.SGI/930901.SGI) for CHEMISTRY@ccl.net id AA15160; Mon, 25 Jul 94 14:34:07 -0700 Received: from localhost by agouron (8.6.4.2/10.3) id OAA22939; Mon, 25 Jul 1994 14:34:04 -0700 Date: Mon, 25 Jul 1994 14:34:04 -0700 From: hou@agouron (Xinjun "Jason" Hou) Message-Id: <199407252134.OAA22939@agouron> To: CHEMISTRY@ccl.net Subject: Hardware benchmarks raeker@tc6.fi.ameslab.gov (Todd J. Raeker) writes: > I will be purchasing at least 2 high performance workstations >... >As I write this I realize that most likely these types of questions >come up periodically. Being that most people on this list are ussually >involved in similiar searchs, it might be a good idea to maintain some >sort of FAQ summarizing the real life performance of workstations. If >there is any interest and one does not already exist, I will volunteer >to maintain such a file that would be available via ftp. Let me know >what you think. Several sites contain benchmark information on various hardwares, many benchmarks are not comp. chem. specific: 1) PDS, "The Performance Database Server", http://performance.netlib.org/performance/html/PDStop.html - a lot of information 2) Anonymous ftp: "ftp.nosc.mil" in "pub/aburto" - bechmarks reported by individual users + ... 3) netlib@ornl.gov (gopher: netlib2.cs.utk.edu 70) in benchmarks/performance directory - LINPACK (from the oldest machine to the newest ones) 4) "comp.benchmarks" newsgroup - regular posting of FAQ.benchmarks and other things Xinjun C Xinjun Jason Hou hou@agouron.com C Agouron Pharmaceuticals, Inc. #include C10110000110100101101110011010100111010101101110010010000110111101110101 From wei@qscat.chem.uh.edu Mon Jul 25 22:56:28 1994 Received: from qscat.chem.uh.edu for wei@qscat.chem.uh.edu by www.ccl.net (8.6.9/930601.1506) id WAA11523; Mon, 25 Jul 1994 22:12:54 -0400 Received: by qscat.chem.uh.edu (AIX 3.2/UCB 5.64/4.03) id AA12807; Mon, 25 Jul 1994 20:49:57 -0500 Date: Mon, 25 Jul 1994 20:49:57 -0500 From: wei@qscat.chem.uh.edu (wei) Message-Id: <9407260149.AA12807@qscat.chem.uh.edu> To: chemistry@ccl.net Subject: DMBE Hi Netters, If some one could offer me the code (subroutine) for Double-Many-Body-Expansion potential surface of H+H2 system? Thanks for any hp. Wei