From OLIVER@psipsy.uct.ac.za Tue Mar 29 05:02:21 1994 Received: from ucthpx.uct.ac.za for OLIVER@psipsy.uct.ac.za by www.ccl.net (8.6.4/930601.1506) id EAA13318; Tue, 29 Mar 1994 04:21:16 -0500 Received: by ucthpx.uct.ac.za (/\==/\ Smail3.1.28.1 #28.8) id m0plZxQ-000KGYC; Tue, 29 Mar 94 11:19 SAST Received: From ITS/WORKQ3 by charongw3.uct.ac.za via Charon-4.0A-VROOM with IPX id 100.940329111615.448; 29 Mar 94 11:18:35 -0200 Message-ID: To: chemistry@ccl.net From: "Hill, RO, Oliver, HLLROB010" Date: Tue, 29 Mar 1994 11:14:47 SAST-2 Subject: PRDDO (Summary) Priority: normal X-mailer: WinPMail v1.0 (R1) A while ago I posted a request for information about the PRDDO (Partial Retention of Diatomic Differential Overlap) method. I got only a few responses (Thanks to those who did), but managed to contact the main author (thanks to David W. Elrod for introducing me to Netfind) and get information on the program. My original posting and the responses follow: ----------------------- Original message ------------------------- Dear Modellers I have recently started using GAMESS (US) to study organometallic systems. I have been digging out various papers and have found one which refers to the PRDDO method (Partial Retention of Diatomic Differential Overlap). The authors use the method for geometry optimization and transition state location, followed by GAMESS for single points. The results look pretty good and the speed is especially impressive. My question is what do people "in the know" think of this method and how many people are using it? Also how does it compare with methods such as ZINDO (INDO/1 & INDO/S)? (It's supposed to extend the approach taken in the CNDO, INDO and NDDO methods by allowing PRDDO). I'd very much like to get hold of the program, so if anyone has that information I'd appreciate that as well. I have tried without success to find the E-Mail address of the authors of the paper I have (Dennis Marynick et al at Univ. of Texas at Arlington). The paper I have is "Potential Energy Surface for Methyl Migration in Tetracarbonylmethylcobalt(I) and Dicarbonylcyclopentadienylmethyliron(II)", Jimmy R. Rogers, Ojin Kwon and Dennis S. Marynick*, Organometallics, 1991, 10, 2816-2823. The original paper for the method is "Self-consistent- field wavefunctions for complex molecules. The approximation of partial retention of diatomic differential overlap", Thomas A. Halgren* and William N. Lipscomb, J. Chem. Phys., Vol 58, No 4, 1973, 1569-1591. Information on any other papers on (or using) the method would be welcomed. Please E-mail me direct (to save bandwidth) and I will summerize to the list. ANY and ALL comments welcome. Thanks in Advance Oliver ______________________________________________________________________ | Oliver Hill | | | Department of Chemistry | "The true scientist never | | University of Cape Town | loses the faculty of | | Rondebosch, 7700 | amazement. It is the essence | | SOUTH AFRICA | of his being." | | OLIVER@PSIPSY.UCT.AC.ZA (internet) | - HANS SELYE | | | | | Tel. +27-21-650-2527 | | | Fax. +27-21-650-3788 | | |____________________________________|_______________________________| ----------------------------- Responses ----------------------------- Date: Thu, 10 Mar 94 08:38:12 -0500 Reply-To: mckelvey@Kodak.COM From: mckelvey@Kodak.COM To: "OLIVER@psipsy.uct.ac.za"@Kodak.COM Subject: RE: CCL:PRDDO Method ?? The principle source is Marynick in the paper you cited... John McKelvey Eastman Kodak ---------------------------------------------------------------------- Date: Thu, 10 Mar 1994 18:38:45 +0100 (WET) From: "Konrad, IRBM Chemistry, +39-6-91093606" To: OLIVER@PSIPSY.UCT.AC.ZA CC: KOEHLER@IRBM.IT Subject: PRDDO Dear Mr. Hill: Please find Dr. Marynick's address below. PRDDO may be obtained through Dr. Marynick. We (especially Jim Snyder of our Institute, snyder@irbm.it) have used PRDDO for many years and have obtained good results for a number of systems. The methods seems most attactive for very large systems where ab initio methods are not pratical. Normally what we do is use one of the standard semiemprical methods to determine a starting geometry followed by a single point PRDDO calculation to obtain the electronic properties and relative energies of the molecule. We have also been in contact with Warren Hehre at Wavefunction, Inc. and he has agreed in principle to provide an interface between Spartan and PRDDO. Dr. Dennis S. Marynick The University of Texas at Arlington Department of Chemistry and Biochemistry BOX 19065 Arlington, TX 76019-0063 U.S.A. telephone: (817) 273-3171 fax: (817) 273-3808 internet: dennis@utadsm2.uta.edu (Dennis S. Marynick) I hope this helps. Sincerely, ------------------------------------------------------------------ | Konrad Koehler | Computational Chemistry Group | | internet: koehler@irbm.it | Department of Medicinal Chemistry | | | IRBM | | telephone: +39-6-910-93606 | Via Pontina Km. 30,600 | | fax: +39-6-910-93225 | 00040 Pomezia (Roma) | | | Italy | ------------------------------------------------------------------ ---------------------------- End ---------------------------------- I found Dr Marynick very willing to provide information about his program, however he prefers me not to include my private correspondence with him here. He asks that anyone interested in the method contact him directly at: "dennis@utadsm2.uta.edu (Dennis S. Marynick)". Oliver Hill ______________________________________________________________________ | Oliver Hill | | | Department of Chemistry | "The true scientist never | | University of Cape Town | loses the faculty of | | Rondebosch, 7700 | amazement. It is the essence | | SOUTH AFRICA | of his being." | | OLIVER@PSIPSY.UCT.AC.ZA (internet) | - HANS SELYE | | | | | Tel. +27-21-650-2527 | | | Fax. +27-21-650-3788 | | |____________________________________|_______________________________| From Patrick.Bultinck@rug.ac.be Tue Mar 29 10:02:33 1994 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.4/930601.1506) id JAA16526; Tue, 29 Mar 1994 09:18:45 -0500 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA11460 (5.65c/IDA-1.4.4 for ); Tue, 29 Mar 1994 16:18:08 +0200 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA09528; Tue, 29 Mar 94 16:15:13 +0200 Date: Tue, 29 Mar 1994 16:15:12 +0200 (MET DST) From: Patrick Bultinck Subject: Textbooks on Comp. Chem. Techniques To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 3028 Dear Netters, I recently posted a question on 1) What is a good book on the technical aspects of making a Hartree-Fock program. 2) Are there HF-SCF programs written in C. I wish to thank everybody who gave me references and suggestions Answer to question 1 : Attila Szabo and Neil S. Ostlund, Modern Quantum Chemistry, Introduction to Electronic structure theory, MacGraw Hill, 1989 (ISBN 0-07-062739-8) This book is mentionned by about everybody who sent a reaction It has now arrived at our laboratory since we had ordered it as a good book on the pure theory of Hartree-Fock. So it is recommended as a reference for the Hartree-Fock theory (we are going to use it as the second text book for the chemistry students (after Levine's book and before Daudel's)) and as a good book for the practice of HF calculus. Following books were recommended Jeffry D. Madura : (I have left some out, since I know them, but do not find them 100% useful for the topic of technical info,comments on this book are purely my opinion) A computational approach to chemistry, David M. Hirst, Blackwell scientific Publ., Oxford, 1990 A handbook of computational chemistry, A practical guide to chemical structure and Energy calculations, T. Clark, Wiley Interscience, 1985 This book is referred to in e.g. the GAMESS (US) documentation as a good book to learn all about Z-matrices. I have seen it in the library of another university, it looks interesting. Computational Chemistry using the PC, D.W. Rogers, VCH, 1990 (comes with disks) Exploring chemistry with electronic structure methods, A guide to using Gaussian, Foresman and Frisch, Gaussian Inc. The fact that this is a book primarily for use together with GAUSSIAN scares me a little (how big is the program dependance ??) Experiments in Computational Organic Chemistry, Hehre Burk Schusterman and Pietro, Wave- function Inc., Irvine E. Lewars suggests : Approximate Molecular Orbital theory, Pople and Beveridge, McGraw Hill 1970 E. Lewars points out that the code might be a little oldfashioned. Answers to question 2 : I haven't received a lot of answers to this question, so it is probably not worth sending a summary... Those wishing to know what messages I got should contact me through E-mail. Thanks again, |-----------------------------------------------------------------------| | C-C Patrick Bultinck | | / \ Dept. Physical & Inorganic Chemistry | | C-O O-C Section Quantum Chemistry | | | | University of Ghent | | C-O O-C Krijgslaan 281 (S-3) | | \ / 9000 Gent | | C-C Belgium | | Tel. Int'l code/32/9/264.44.44 | | Macrocycles Fax. Int'l code/32/9/264.49.83 | | Quantumchemical E-mail : Patrick.Bultinck@rug.ac.be | | Calculations | |-----------------------------------------------------------------------| From SATYAM@vms.cis.pitt.edu Tue Mar 29 11:01:55 1994 Received: from VM2.CIS.PITT.EDU for SATYAM@vms.cis.pitt.edu by www.ccl.net (8.6.4/930601.1506) id LAA17881; Tue, 29 Mar 1994 11:01:17 -0500 From: Received: from vms.cis.pitt.edu by vms.cis.pitt.edu (PMDF V4.2-14 #4065) id <01HAJIMWYCGGC51KGH@vms.cis.pitt.edu>; Tue, 29 Mar 1994 11:01:10 EST Date: Tue, 29 Mar 1994 11:01:10 -0500 (EST) Subject: cuestion from computational chemist..for software/hardware help.. To: CHEMISTRY@ccl.net Message-id: <01HAJIMX07Z6C51KGH@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 Fellow netters, We want to print some molecular structures from using software on Macintosh..on to a color/b&w laser printer connected to an SGI machine with internet address..also Mac has an internet address... We are aware of ftp -ing the file..but thats a slow process.... We want to know if there is some software/hardware..so that the Mac PRINT command send's it to SGI--lpr queue.... Looking forward to replies... Thanks Satyam ((( satyam@vms.cis.pitt.edu /// satyam@hathi.chem.pitt.edu ))) From terry@wag.caltech.edu Tue Mar 29 12:01:55 1994 Received: from brahms.wag.caltech.edu for terry@wag.caltech.edu by www.ccl.net (8.6.4/930601.1506) id LAA18172; Tue, 29 Mar 1994 11:29:27 -0500 Received: by brahms.wag.caltech.edu id AA04989 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Tue, 29 Mar 1994 08:29:25 -0800 Date: Tue, 29 Mar 1994 08:29:25 -0800 From: "Terry R. Coley" Message-Id: <199403291629.AA04989@brahms.wag.caltech.edu> To: chemistry@ccl.net Subject: SUMMARY: peak separation/fitting software Last week, I posted a request for information on peak separation/fitting software appropriate to UV/Vis spectra. I received two quotable responses which I've included below. I've also received surface mail literature and demo disk for the GRAMS/386 software. Although I have not evaluated it yet, the software appears to be very useful. Thank you to all who responded. - Terry Terry R. Coley, Ph.D. terry@wag.caltech.edu 818-395-2723 Caltech, M/S 139-74 Pasadena, CA 91125 ----- Begin Included Message ----- [email address excluded at sender's request] I use GRAMS/386 which runs under MS-Windows. It has many instrument file format converters and generic import and export converters such as ASCII_XY, ASCII_Y and they recently added OBDC features, too. Thus, GRAMS can probably read the data you want to work with with no or little effort. Under GRAMS you can do baseline subtraction with a straight line or via a polynomial you graphically fit to baseline points. You can also do fourier self-deconvolution, interpolation, increase the resolution on a spline, zero fill, decrease the resolution, adjust point spacing to user defined intervals and more. GRAMS also has a feature called "Curve Fit" which uses the Levenberg-Marquadrt method to fit ideal peaks to your experimental data. There is also a thrid party accessory to GRAMS which provides maximum likelihood, maximum entropy, and others, resolution enhancement tools. GRAMS is also extendable by user in that it has a language, ARRAY BASIC, which is a derivative of basic but is optimzed for dealing with spectra and chromatograms. It also comes with some nifty Windows user interface tools. GRAMS is written by Galactic Industries. They can give you all the price information at 1-800-862-6004, 1-603-898-7600 or fax 1-603-898-6228. Best Regards, -Will Costa =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= William Costa Fiveash Data Management phone: 414-563-6449 400 Madison Avenue FDM deals in reference spectra databases and P. O. Box 400 related chemical information. Fort Atkinson, WI 53538 USA =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= ----- End Included Message ----- ----- Begin Included Message ----- From DLICHTEN@ccit.arizona.edu Wed Mar 23 07:58:47 1994 Received: from SkyBlu.CCIT.Arizona.EDU by sgi1 with SMTP id AA07817 (931110.SGI/IDA-1.4.4); Wed, 23 Mar 94 07:58:47 -0800 Received: from CCIT.ARIZONA.EDU by CCIT.ARIZONA.EDU (PMDF V4.2-13 #2381) id <01HAB0I7RFKW8WXLDF@CCIT.ARIZONA.EDU>; Wed, 23 Mar 1994 08:58:12 MST Date: Wed, 23 Mar 1994 08:58:11 -0700 (MST) From: "DENNIS L. LICHTENBERGER" Subject: fitting software To: terry@wag.caltech.edu Message-Id: <01HAB0I7SI5U8WXLDF@CCIT.ARIZONA.EDU> X-Envelope-To: terry@wag.caltech.edu X-Vms-To: IN%"terry@wag.caltech.edu" X-Vms-Cc: DLICHTEN Mime-Version: 1.0 Content-Transfer-Encoding: 7BIT Status: RO In answer to your question about fitting software for UV/VIS absorption spectra, we have developed over a period of about 20 years a fitting package for photoelectron spectroscopy that should work just as well for UV/Vis because the same principles are involved. Take a look at the Journal of Electron Spectroscopy and Related Phenomena, Volume 50, 1990, pages 335-352. Our present versions of these programs are in basic and run on PCs. Earlier versions were programmed in Fortran, were more crude, and ran on VMS machines. Let me know if you are interested. Dennis Lichtenberger Professor of Chemistry University of Arizona ----- End Included Message ----- From C1790@SLVAXA.UMSL.EDU Tue Mar 29 12:04:58 1994 Received: from SLVAXA for C1790@SLVAXA.UMSL.EDU by www.ccl.net (8.6.4/930601.1506) id LAA18085; Tue, 29 Mar 1994 11:21:16 -0500 From: Received: from SLVAXA.UMSL.EDU by SLVAXA.UMSL.EDU (PMDF V4.2-11 #2503) id <01HAJHE744689ZM2L9@SLVAXA.UMSL.EDU>; Tue, 29 Mar 1994 10:20:46 CST Date: Tue, 29 Mar 1994 10:20:46 -0600 (CST) Subject: RESPONSES TO INQUIRY ON A TEXTBOOK FOR COMPUT. CHEM. COURSE To: CHEMISTRY@ccl.net Message-id: <01HAJHE74X429ZM2L9@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 >FROM BILL WELSH [UNIV. OF MISSOURI-ST. LOUIS]: A FEW WEEKS AGO I ASKED FOR RECOMMENDATIONS ON A TEXTBOOK FOR A (BEGINNER) GRADUATE COURSE IN COMPUTATIONAL CHEMISTRY. I WANT TO THANK THE MANY PEOPLE WHO PROVIDED VALUABLE RESPONSES. GIVEN THE LARGE NUMBER OF RESPONSES TO MY INQUIRY, I THOUGHT IT APPROPRIATE TO SHARE THE EDITED RESPONSES WITH MY COLLEAGUES ON THE NETWORK BULLETIN BOARD. SO HERE IT GOES .... For a practical guide to ab initio quantum chemistry, I have found the guide from Gaussian Inc. ("Exploring Chemistry with Electronic Structure Methods: A Guide to Using Gaussian") to be quite good. In addition, NIH appears to be developing an "electronic textbook" for molecular modeling. Some of the information is specific to the NIH site, but much of it is more general. To take a look at it, access their Mosaic server at http://www.nih.gov. ****************************************************************************** The book titled "Experiments in Computational Organic Chemistry" by W. J. Hehre, L. D. Burke, A. J. Shusterman and W. J. Pietro would be a very good one to look into. It is also fairly inexpensive (which your students would appreciate). __________________________________________________________ The best modern book is a little gem from Warren Hehre's people at Wavefunction, Inc (714.955.2120). The name of the book is: "Experiments in Computational Organic Chemistry", Warren J. Hehre, Lonnie D. Burke, Alan J. Shusterman and William J. Pietro. They are privately publishing this, but I'm sure he would give you a few copies to check out... Warren is making it available at pretty low prices (on the order of $10-15 a copy), so I would check with him... -------------------------------------------------------------------------- The book titled "Experiments in Computational Organic Chemistry" by W. J. Hehre, L. D. Burke, A. J. Shusterman and W. J. Pietro would be a very good one to look into. It is also fairly inexpensive (which your students would appreciate). __________________________________________________________ I have been looking at texts with a purpose similar to yours in mind. So far the best ones I have come up with are "Experiments in Computational Organic Chemistry" by W.J. Hehre, L.D. Burke, A.J. Shusterman, and W.J. Pietro and "Computational Simulations of Liquids" by Allen and Tildesley but even these have their shortcomings. Then, at a more advanced level, you might consider "Quantum Chemistry, 2nd edition" by J.P. Lowe It has nice homehowrk problems in quantum chemistry that explain how basis set methods work. I also like "Computational Quantum Chemistry" by A. Hinchliffe but it has no homework problems. In our physical chemistry sequence I use MacQuarrie's "Quantum Chemistry" for the first semester of pchem and our advanced pchem course (third semester) involves using computational methods...for that course I plan to use Hehre et.al., allen and Tildesley, and possibly Hinchcliffe (the first two texts are available in paperback). ******************************************* A very good text for ab initio calculations is by Szabo and Ostlund, "Modern Quantum Chemistry" isbn 0-07-062739-8 McGraw Hill 1-800-2-MCGRAW. I used this text when I took a graduate level quantum chemistry. I highly recomend it for students who have had at least a semester of quantum mechanics. I recommend "Exploring Chemistry with Electronic Structure Methods" by Foresman & Frisch. It can be obtained from Gaussian Inc. info@gaussian.com Bill, there are two which spring imediately to mind. 1. Exploring Chemistry with Electronic Structure methods: a guide to Gaussian James B. Foresman and AE Frisch Available from Gaussian Inc ISBN: 0-9636769-0-3 2. Experiments in Computational Organic Chemistry Warren J. Herre and Lonnie D. Burke and Alan J. Shusterman and William J. Pietro available form Wavefunction Inc. While both have their own axes to grind (gaussian vs spartan) both are just what you are after. They are also not terribly expensive. Here is a suggestion. I have used the book: " Molecular Dynamics Simulation: Elementary methods" by J. M. Haile. It was written in 1992, and has exercises at the end of each chapter. I find it very helpful. Since I don't have a comprehensive reference, some recommendations for the quantum portion are. 1. Quantum Chemistry by McQuarrie (undergraduate) 2. quantum Chemistry by Levine (graduate) 3. Exploring Chemistry with Electronic Structure Methods This is a users companion to Gaussian. Available directly from Gaussian Inc. [FROM PHIL BOWEN, UNIV. OF GEORGIA] I do not have a book solution for this year's class, but soon there will be a text available that you can use next year. I will be writing and editing a textbook on this subject entitled "Methods and Techniques of Molecular Modeling". The text is being published by Oxford University Press. In addition to my writing, there will be chapters contributed by the following: N. L. Allinger, Charles Brooks, III, Lee Pedersen, Lee Bartolotti, Matt Clark, Alan Richon, and Bob Pearlman. The book is an introductory text designed for advanced undergraduates and first year graduate students. There will be a separate problems manual to accompany the textbook. I hope that this book will help to serve your needs once it is published and available. It seems that my reply to the request for a computational chemistry book has elicited some interest. For those of you who are interested, it is put out by Wavefunction, Inc. Their phone number is (714) 955-2120 and their FAX number is (714) 955-2118. Their is no edition number listed in the book (copyright 1993). It was written to be compatible with the abilities of SPARTAN, though the experiments described within it are certainly not limited to that software. __________________________________________________________ "Experiments in Computational Orgenic Chemistry", by Hehre, Burke, Shusterman and Pietro, which has recently been recommended on the net, is an excellent book for showing the capabilities of computational chem in hands-on work. It works most naturally with Wavefunction's SPARTAN program, but should be adaptable to, e.g. Gaussian with some success. "Exploring Chemistry With Electronic Structure Methods" by Foresman and A. Frisch of Gaussian Inc is a very instructive book for those getting into comp chem. Unlike the Wavefunction book, it is devoted essentially entirely to ab initio calculations ("Experiments.." deals with mechanics, semiemp and ab initio), and input is limited to the Z-matrix (with a nod at cartesians), while results must be interpreted by poring over the printed output, unless you are lucky enough to have a program that will create Gaussian input from mousedrawn structures, and bring wavefunctions to life, animate normal modes, etc etc. But "Exploring...." has plenty of valuanble information, and is well worth reading [students read studying]. As for software, the only integrated MM, semiempirical, ab initio cum supergraphics comp chem program I am aware of is SPARTAN. I teach a course in Molecular Modeling of Proteins and have encountered the same difficulty as you in finding a suitable text. I had sent a response to your message indicating a couple of sources that may be useful. Another article that you may want to look at is by Harvey and Tan, "Teaching macromolecular modeling", Biophys. J. 63, 1683-1688, Dec 1992. ****************************************************************************** A good book to start with is: Clark, A handbook of computational chemistry: a practical guide to chemical structure and energy calculations, Wiley, 1985. You can't go past the (now) five volumes of "Reviews in Computational Chemistry" edited by Kenny Lipkowitz and Don Boyd, VCH 1990-1994 ISBN (vol 1) 0-89573-754-X VCH. Has an appendix with info an all current modelling etc software. From silviu@chemib5.tau.ac.il Tue Mar 29 13:01:57 1994 Received: from chemib5.tau.ac.il for silviu@chemib5.tau.ac.il by www.ccl.net (8.6.4/930601.1506) id MAA18443; Tue, 29 Mar 1994 12:04:08 -0500 From: Received: by chemib5.tau.ac.il (AIX 3.2/UCB 5.64/4.03) id AA21277; Tue, 29 Mar 1994 16:34:18 +0100 Date: Tue, 29 Mar 1994 16:34:13 +0100 (NFT) Sender: silviu@chemib5.tau.ac.il Reply-To: silviu@chemib5.tau.ac.il Subject: MD C++ class libraries To: computational chemistry Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear netters, I'm looking for information about Object - Oriented Molecular Dynamics simulations done in C++. The questions I seek to answer are: 1. Are there some people who tried using C++ for MD simulations of fluids, and what is their opinion about the applicability of the Object Oriented paradigm for MD simulations. I'm especially interested in the aspects of re-using the code and the ability to preduce increasingly more complex simulations from simple classes through inheritance mechanism. 2. Are there any public class libraries for MD simulations of fluids that I can get and try ? 3. Are there any public mathematical class libraries ? I would very much appreciate answers from anyone who can contribute, and I'll summerize the results. e-mail for answers: silviu@chemib5.tau.ac.il Silviu Zilberman From carlos@pap.chem.uic.edu Tue Mar 29 13:04:39 1994 Received: from slipknot for carlos@pap.chem.uic.edu by www.ccl.net (8.6.4/930601.1506) id MAA18545; Tue, 29 Mar 1994 12:07:35 -0500 Received: from pap.chem.uic.edu by slipknot (AIX 3.2/UCB 5.64/4.03) id AA02924; Tue, 29 Mar 1994 11:02:12 -0600 Received: by pap.chem.uic.edu (3.2/SMI-3.0DEV3) id AA22203; Tue, 29 Mar 94 11:13:03 CST Date: Tue, 29 Mar 94 11:13:03 CST From: Carlos Simmerling Message-Id: <9403291713.AA22203@pap.chem.uic.edu> To: chemistry@ccl.net Subject: MOIL-View information Since several people replied to my original message asking for a list of MOIL-View users by asking exactly what MOIL-View is, I will post this directly to the list. MOIL-View Written by Carlos Simmerling **************************************** MOIL-View is a program for Silicon Graphics and IBM RS/6000 workstations designed to allow the user to view a molecular structure. Many of the options have been implemented with the user of MOIL in mind, and some of the routines come directly from the MOIL program. GENERAL FEATURES ---------------- mouse and menu interface read/write CHARMm format CRD files as well as PDB files OPTIONAL use of MOIL connectivity files for bonding information allows rotation,translation etc. of structure DCD-type dynamic files may be read and a movie can be shown compression option for faster playback of complicated dynamics support for NTSC/genlock video display objects as lines, ribbons and/or spheres two molecules may be shown overlap function to minimize rms of selected particles of two molecules user definable colors and particle selection shows distances, angles and torsions find and display hydrogen bonds postscript output of structures and bitmap images print contact maps of molecules full source code (FORTRAN) available for ease of modification Carlos Simmerling University of Illinois at Chicago Department of Chemistry (M/C 111) 845 W. Taylor Street Chicago, IL 60607-7061 carlos@pap.chem.uic.edu From carlos@pap.chem.uic.edu Tue Mar 29 15:02:17 1994 Received: from slipknot for carlos@pap.chem.uic.edu by www.ccl.net (8.6.4/930601.1506) id OAA19841; Tue, 29 Mar 1994 14:32:52 -0500 Received: from pap.chem.uic.edu by slipknot (AIX 3.2/UCB 5.64/4.03) id AA02828; Tue, 29 Mar 1994 13:27:30 -0600 Received: by pap.chem.uic.edu (3.2/SMI-3.0DEV3) id AA22628; Tue, 29 Mar 94 13:38:25 CST Date: Tue, 29 Mar 94 13:38:25 CST From: Carlos Simmerling Message-Id: <9403291938.AA22628@pap.chem.uic.edu> To: chemistry@ccl.net Subject: MOIL-View Dear CCLers, Several people have pointed out to me that I did not mention how to obtain MOIL-View! Full source and documentation are available through anonymous ftp to 128.248.186.70. You will want to get (in the directory 'dist'): README.moil-view moil-view_v7.4.doc moil-view_v7.4.???.src.tar.Z (where ??? is sgi or ibm) there is also an SGI binary file for those without FORTRAN. Carlos Simmerling From d3g359@rahman.pnl.gov Tue Mar 29 16:02:17 1994 Received: from pnlg.pnl.gov for d3g359@rahman.pnl.gov by www.ccl.net (8.6.4/930601.1506) id PAA20682; Tue, 29 Mar 1994 15:47:12 -0500 From: Received: from rahman.pnl.gov (130.20.182.20) by pnlg.pnl.gov; Tue, 29 Mar 94 12:42 PST Received: by rahman.pnl.gov (920330.SGI/890607.SGI) id AA15970; Tue, 29 Mar 94 12:42:15 -0800 Date: Tue, 29 Mar 94 12:42:15 -0800 Subject: G92 SCRF Calcs To: CHEMISTRY@ccl.net Message-id: <9403292042.AA15970@rahman.pnl.gov> X-Envelope-to: CHEMISTRY@ccl.net Hi, Can someone please share there experience with SCRF calculations in g92? I'd like to know the following: 1. What exactly each of the different energy values that gaussian prints out correspond to computationally. 2. The sensitivity of the calculated values to the cavity radius. Too small a radius is clearly a problem, but what happens when you make it large? 3. Should one attempt to use the same radius for two different conformations (of slightly differing size) of the same molecule or two different arragements of groups of molecules? 4. Why is there no (apparently) polarization stabilization for anions? I have not tried cations. Thanks, John ------------------------------------------------------------------------------ John Nicholas Office: (509) 375-6559 Senior Research Scientist FAX: (509) 375-6631 Molecular Science Research Center Pacific Northwest Laboratory Mailstop K1-90 Richland, WA 99352 ------------------------------------------------------------------------------ From haldi@acpub.duke.edu Tue Mar 29 17:02:00 1994 Received: from raphael.acpub.duke.edu for haldi@acpub.duke.edu by www.ccl.net (8.6.4/930601.1506) id QAA21455; Tue, 29 Mar 1994 16:56:04 -0500 Received: from localhost (haldi@localhost) by raphael.acpub.duke.edu (8.6.4/Duke-1.1) id QAA14686; Tue, 29 Mar 1994 16:55:59 -0500 Date: Tue, 29 Mar 1994 16:54:53 -0500 (EST) From: John Haldi Subject: subscription request To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I would appreciate it if you would include me on your mailing list in the future. Thank you very much. Sincerely, John Haldi North Carolina Analytics 4800 University Drive, #16H Durham, NC 27707 haldi@acpub.duke.edu