From SANTOS@BMSUEM11.bitnet Tue Mar 2 14:13:34 1993 Message-Id: <199303021326.AA17970@oscsunb.ccl.net> Date: Tue, 02 Mar 93 14:13:34 GMT From: "D.A. dos Santos" Subject: MOPAC 7 To: chemistry@ccl.net Dear Netters, I would like to ask a question about the new version of MOPAC (MOPAC 7). Is it already available? Who should I contact to get more information about it? I've tried the software index but I haven't found anything corcerning MOPAC 7. Thanks a lot in advance, Donizetti dos Santos Service de Chimie des Materiaux Nouveaux Universite Mons Hainaut Belgium From pc1@pctc.chemie.uni-erlangen.de Tue Mar 2 15:16:51 1993 Date: Tue, 2 Mar 1993 14:16:51 +0100 From: pc1@pctc.chemie.uni-erlangen.de Message-Id: <9303021316.AA15198@pc1.chemie.uni-erlangen.de> To: chemistry@ccl.net Subject: Expert Know-How wanted !! Hello, I plan to implement a routine in one of my programs, to convert geometry information in xyz-coordinates into internal coordinates. This is usually done by programs like PCModel in a way that seems not to be very satisfying. I think about an algorithm, that is based on some general rules, from which a Z-matrix would be created, that is more similar to one created by human-beings. So I would like to hear what you think are good ways of writing a Z-matrix (e.g. for aromatic systems, methyl-groups, ...). Thank you very much in advance, I will summarize the response for the net. Peter Gedeck gedeck@pctc.chemie.uni-erlangen.de From BOYD_DONALD_B@INET.D48.LILLY.COM Tue Mar 2 03:13:18 1993 Date: 02 Mar 1993 08:13:18 -0500 (EST) From: "DONALD B. BOYD" Subject: new book on computational chemistry To: chemistry@ccl.net Message-Id: <01GVBQOJBES28WVZ2K@INET.D48.LILLY.COM> Volume 4 of REVIEWS IN COMPUTATIONAL CHEMISTRY has been published. It addresses questions, such as: Should large molecules be calculated by semiempirical or ab initio quantum methods? What is the best way to locate a transition state on a potential energy surface? What is the state of the art in computing solution state reaction dynamics? How is computational chemistry being taught at colleges and universities? The chapters and authors are -- "Ab Initio Calculations on Large Molecules: Methodology and Applications" by Jerzy Cioslowski (Florida State University), "Computing Reaction Pathways on Molecular Potential Energy Surfaces" by Michael L. McKee (Auburn University) and Michael Page (North Dakota State University), "Computational Molecular Dynamics of Chemical Reactions in Solution" by Robert M. Whitnell and Kent R. Wilson (University of California at San Diego), and "Computational Chemistry in the Undergraduate Curriculum" by Roger L. DeKock (Calvin College), Jeffry D. Madura (University of South Alabama), Frank Rioux (St. John's University), and Joseph Casanova (California State University at Los Angeles). REVIEWS IN COMPUTATIONAL CHEMISTRY is edited by K. B. Lipkowitz (IUPUI) and Donald B. Boyd (Lilly Research Laboratories). The series aims to bring together renowned experts to give accounts of research in the many facets of computer-aided chemistry, such as molecular modeling, computer-assisted molecular design (CAMD), quantum chemistry, molecular mechanics and dynamics, and quantitative structure-activity relationships (QSAR). Many chapters in the series are written as tutorials for beginners. Included in each volume is a continually updated, comprehensive compendium of software. Listed are hundreds of programs, services, suppliers, and other helpful information. Information about Volume 4 (280 pp, ISBN 1-56081-620-1, 1993) can be obtained from VCH Publishers, Inc., 303 NW 12th Avenue, Deerfield Beach, Florida 33442. In the U.S., call 800-367-8249, FAX: 1-800-367-8247; in Europe, 49-6201-6060, FAX: 49-6201-606328. Price $79. With a standing order for the book series, the price is $65. Volume 3 of REVIEWS IN COMPUTATIONAL CHEMISTRY was released in December, 1992. From: BOYD DONALD B (MCVAX0::QSAR) To: VMS MAIL ADDRESSEE (INT::"chemistry@ccl.net") cc: BOYD DONALD B (MCVAX0::QSAR) From jstewart@fujitsu.fai.com Mon Mar 1 22:42:28 1993 Date: Tue, 2 Mar 93 06:42:28 PST From: jstewart@fai.com (Dr. James Stewart) Message-Id: <9303021442.AA22607@fujitsu.fai.com> To: chemistry@ccl.net Subject: MOPAC 7, renamed MOPAC 93 MOPAC 7 is now complete. It's name has been changed to MOPAC 93. It will be distributed through QCPE, at the same cost as MOPAC 6.0. There are still one or two small details to be resolved before it can be generally distributed, however. As soon as these points are resolved, MOPAC 93 will be distributed by QCPE. Jimmy Stewart From RDJ3@ENH.NIST.GOV Tue Mar 2 07:29:30 1993 Date: 02 Mar 1993 11:29:30 -0400 (EDT) From: RDJ3@ENH.NIST.GOV Subject: RE Benson's Rules To: CHEMISTRY@ccl.net Message-Id: <01GVBXH8BP4M008Z29@ENH.NIST.GOV> The National Institute of Standards and Technolgy (NIST) has a database for PCs which can estimate thermochemical values from a drawn structure using Benson's rules. It is the Sturctures and Properties Database. The price tag is $240. Contact : Joan Sauerwein phone : 301+975-2208 fax : 301+926-0416 From DSMITH@uoft02.utoledo.edu Tue Mar 2 07:36:08 1993 Date: Tue, 02 Mar 1993 12:36:08 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: DEC Alpha workstations/servers To: chemistry@ccl.net Message-Id: <01GVBZTHS142000NCO@UOFT02.UTOLEDO.EDU> Are there any commercial software vendors writing for the Alpha, under either OpenVMS or (preferably) OSF/1? Are they/you writing for the graphics workstation and for what level of graphics? Or is anyone writing for the Alpha as a non-graphical server? Please don't respond about public domain or QCPE software - we do that under a grant from DEC and supply the ports to QCPE ourselves. About 30 programs ought to show up soon. Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From ravishan@swan.wesleyan.edu Tue Mar 2 08:22:16 1993 Date: Tue, 2 Mar 93 13:22:16 -0500 Message-Id: <9303021822.AA15982@swan.wesleyan.edu> From: G. Ravishanker To: chemistry@ccl.net Subject: Charge groups Hi I would like to gather some information on the possibility of using charge groups and the protocols used in determining the energy/forces amongst them in an MD simulation. We use GROMOS-type model exclusively, where neutral charge groups are predefined in the Molecular Topology File. Non-bonded interactions are calculated as follows: 1. Determine the geometric center of the charge groups. 2. Calculate the distance between the charge group centers to determine if they are within the cutoff, and whether the distance is in the switching function region. 3. If interaction needs to be calculated, then all pair interactions between atoms in each charge group is evaluated using the ATOM-ATOM distance. 4. If they fall in the switching region, a SINGLE switching function value based on the charge group center distance is applied to all ATOM-ATOM interactions. I would like to know: 1. How do AMBER, CHARMM and GROMOS87 handle the charge groups. 2. How exactly are the determination of whether a particular group-group interaction needs to be included is determined - based on charge group centers, or based on whether any two atoms in the charge groups falling within the cutoff or by any other criterion. 3. What switching function is applied? 4. In case of distance dependent dielectric type approximation, what distance is used? I would very much appreciate hearing from anyone who can provide these information and I will gladly summarize any information that I recieve. Thank you for your time. Ravi **************************************************************************** * Ganesan Ravishanker Ph: (203) 344-8544 Ext. 3110 * * Coordinator of Scientific Computing, Fax:(203) 344-7960 * * Adjunct Associate Professor(Dept. of Chem.) * * Wesleyan University e-mail:ravishan@swan.wesleyan.edu * * Middletown, CT 06457. * **************************************************************************** From aec@howdy.wustl.edu Tue Mar 2 07:23:57 1993 Date: Tue, 2 Mar 1993 13:23:57 -0600 From: "Anders E. Carlsson" Message-Id: <199303021923.AA13191@howdy.wustl.edu> To: chemistry@ccl.net Subject: Molecular Visualization To whom it may concern: I am looking for public-domain software for visualizing molecules and solids. I would like each atom to be represented by a sphere (preferably directionally shaded), and also to have the possibility of putting sticks between the spheres (ball-and-stick models) when I choose. Preferably, the software should run on SGI and IBM Risc machines with X-windows, but if it only runs on SGI machines that is still useful. Thank you, Anders Carlsson From newton%gandal.dnet@server.uga.edu Tue Mar 2 10:30:30 1993 Date: Tue, 2 Mar 93 15:30:30 -0500 Message-Id: <9303022030.AA02605@server.uga.edu> From: newton%gandal.dnet@server.uga.edu To: "chemistry@ccl.net"%SERVER.dnet@server.uga.edu Subject: Summary of Benson rule programs Dear Netters: Several days ago I posed the following: "Do any programs exist which estimate thermochemical values from an input structure diagram using Benson's additivity rules (or any other scheme)? Gary Newton UGa E-MAIL newton@bscf.uga.edu" I received two viable replies, which follow: -------------------------------------------------------------------------- Ed Ritter replied: I have developed a (DOS) computer program called THERM which can be used to estimate thermodynamic properties for radicals and molecules. The program requires a math co-processor on all but 486 machines, and takes up about 1 Mb of space on the hard disk. Ed Ritter - Villanova Univ. e-mail eritter@vill.edu -------------------------------------------------------------------------- Horst Boegel replied: Dear CC- users, 1.3.1993 GARY NEWTON asked : "Do any programs exist which estimate thermochemical values from an input structure diagram using Benson's additivity rules (or any other scheme)? Gary Newton UGa E-MAIL newton@bscf.uga.edu" Yes. We wrote a PC-program for handling chemical structures from a mouse- drawn structural formula with automatic generation of the Connection Table. From this CT we are able to calculate a lot of topological Indices. Up to now the BENSON's schema to predict the Heat of Formation and the Heat Capacity is included. At the moment the structural para- meters for hydrocarbons are implemented. More information from: Horst Boegel: boegel@chemie.th-merseburg.dbp.de or phone: +3461 46 2127 (Germany) --------------------------------------------------------------------------- From caldwell@utdallas.edu Tue Mar 2 10:48:51 1993 From: "Richard A. Caldwell" To: chemistry@ccl.net Subject: allenes in MM2(87)? Message-Id: <93Mar2.164908cst.15785@utdallas.edu> Date: Tue, 2 Mar 1993 16:48:51 -0600 Hi, all! We are trying to estimate the dihedral angles between the phenyls and the vinylidene carbons in tetraphenylallene with MM2(87), which alas appears not to have the allene carbon built in. Does someone have parameters for an allene carbom they could ship me, or a reference, or (greedy!) both? Or am I missing something in the manual? Thanks. Dick Caldwell Department of Chemistry The University of Texas at Dallas caldwell@utdallas.edu From esc1@Ra.MsState.Edu Tue Mar 2 11:22:53 1993 From: esc1@Ra.MsState.Edu (Gene Carter) Message-Id: <9303022322.AA19675@Isis.MsState.Edu> Subject: Co MD parameters. To: chemistry@ccl.net Date: Tue, 2 Mar 93 17:22:53 CST Hello, I am interested in preforming MD calculations on a Cobalt containing biomolecule which features a porphyrin ring structure. I am unable to locate any MD parameters(Force constants, etc.) Have any MD parameters been produced? If so, can some kind soul please point me to a reference? Thanks. -- Gene Carter esc1@ra.msstate.edu Mississippi State esc1@msstate.bitnet From landrum@chemres.tn.cornell.edu Tue Mar 2 15:26:13 1993 Message-Id: <199303030357.AA06003@oscsunb.ccl.net> From: Greg Landrum Subject: Re:CAChe on the Mac To: chemistry@ccl.net Date: Tue, 2 Mar 93 20:26:13 EST I am a grad student in Roald Hoffmann's group here at Cornell. We recently installed a CAChe system in our lab and I have found the system to be quite easy learn. While this is not an educational lab, I think that the CAChe software would work very well in that context. The software is easy enough to use and well enough integrated that it would be no problem for students to learn to make use of it. I believe that this ease of use makes the software well suited to use in an educational lab. I would be happy to answer an specific question you might have. -greg Landrum landrum@chemres.tn.cornell.edu