From chemistry-request@ccl.net Thu Jul 11 10:43:33 1991 Date: Thu, 11 Jul 1991 10:20 EST From: PUDZIANOWSKI@bms.com Subject: CADPAC To: chemistry@ccl.net Status: R I'd greatly appreciate some information about the ab initio program system CADPAC. In particular, how does its functionality compare with GAUSSIAN 90, HONDO, GAMESS; what computers is it available for; what is the cost to commercial institutions; and who distributes it? Many thanks for any help! Andy Pudzianowski Bristol-Myers Squibb PRI Box 4000 Princeton NJ 08543-4000 (609) 921-4248 pudzianowski@bms.com From chemistry-request@ccl.net Thu Jul 11 11:32:58 1991 From: jgolab@ncsa.uiuc.edu (Joseph Golab -Apps) Date: Thu, 11 Jul 1991 10:07:00 CDT To: PUDZIANOWSKI@bms.com Subject: Re: CADPAC Status: R Information about CADPAC can be obtained from Dr. Roger Amos. His Email address is rda1@ukacrl.bitnet. +***********************************************************+ * | * * Joe Golab | jgolab@ncsa.uiuc.edu -OR- * * NCSA - University of Illinois | 12688@ncsavms[.bitnet] * * 4025 Beckman Institute | * * MC 251 - DRAWER 25 | IN CASE OF EMERGENCY: * * 405 North Mathews Avenue | (217) 244 2756 (Voice) * * Urbana, Illinois 61801 | (217) 244-2909 (FAX) * * | * +***********************************************************+ From chemistry-request@ccl.net Thu Jul 11 12:11:33 1991 Date: Thu, 11 Jul 91 11:59:31 -0400 From: zheng@retina.chem.psu.edu (Ya-Jun Zheng) To: PUDZIANOWSKI@bms.com Subject: Re: CADPAC Status: R In general CADPAC is faster than Gaussian series programs. Comparison can be find in a new book--Page 383 of Reviews in Computational Chemistry. You may contact the following people. Dr. Roger D. Amos Dr. N. C. Handy Lynxvale WCIU Programs 20 Trumpington Street Cambridge CB2 1QA U.K. 44-223-336384 Hope this may be useful to you. Ya-Jun Zheng Penn State University From chemistry-request@ccl.net Thu Jul 11 12:35:54 1991 Date: Thu, 11 Jul 91 12:21:06 EDT From: m10!frisch@uunet.UU.NET (Michael Frisch) Subject: CADPAC and Gaussian To: chemistry@ccl.net Status: R uunet!retina.chem.psu.edu!zheng comments: In general CADPAC is faster than Gaussian series programs. Comparison can be find in a new book--Page 383 of Reviews in Computational Chemistry. You may contact the following people. Dr. Roger D. Amos Dr. N. C. Handy Lynxvale WCIU Programs 20 Trumpington Street Cambridge CB2 1QA U.K. 44-223-336384 Hope this may be useful to you. Ya-Jun Zheng Penn State University This is not a fair generalization. Beware of comparisons between CADPAC and obsolete versions of Gaussian. In fact, for most of the subset of Gaussian's capabilities which are present in CADPAC, Gaussian 90 is faster. I would strongly encourage people to make their own comparisons on real jobs, rather than relying on hearsay which may be inaccurate, out of date, or both. Michael Frisch Gaussian, Inc. ------- **** End of Forwarded Message **** ------- From chemistry-request@ccl.net Thu Jul 11 14:07:14 1991 To: chemistry@ccl.net Subject: MM3 Carbon parameters Date: Thu, 11 Jul 91 12:47:12 EDT From: Timothy.Freeman@U.ERGO.CS.CMU.EDU Status: R MM3 has several different parameters for carbon. Can anyone tell me how to figure out which parameters to use for which carbon? More specifically, in "Molecular Mechanics. The MM3 Force Field For Hydrocarbons" by Allinger, Yuh, and Lii (J. Am. Chem. Soc., vol 111 # 23), there is a table on page 8555: (B) Angle Bending theta sub 0 super c ------------------------- atoms K sub theta Type 1 Type 2 Type 3 C-C-C 0.67 109.5 110.2 111.0 C-C-H 0.59 109.8 109.3 110.7 H-C-H 0.55 107.6 107.8 109.5 and so on. The text gives a formula for bending potential energy in terms of k sub theta (that's a little k, even though a big K is in the table) and theta sub 0 (without any superscript). How do I figure out whether a particular carbon is Type 1, Type 2, or Type 3? Thanks, Tim From chemistry-request@ccl.net Thu Jul 11 14:40:39 1991 Date: Thu, 11 Jul 91 13:17:41 CDT From: liberte@ncsa.uiuc.edu (Daniel LaLiberte) To: chemistry@ccl.net Subject: Chemistry Taxonomy Status: R I had asked in May for information on chemistry taxonomies, especially related to object-oriented classification of chemistry concepts. I got a couple responses and phone calls that I will summarize here. I received a call from someone at Molecular Simulation Inc of Sunnyvale CA (used to be Bio-Design). They are developing chemistry tools on a C++ platform, but they are primarily concerned with what I would call "basic chemistry", if I understood correctly. By that I mean definitions of atoms, bonds, molecules, 3D positions, maybe velocities, electron densities, etc, but nothing like classifications of organic and inorganic molecules, reaction types, chemical proceses, and more complex concepts. Two people mentioned SMILES notation not as a taxonomy itself, but as a very concise description of chemical structure connectedness. SMILES can correctly represent structural variations such as isomers, isotopes, chirality, tautomers. Furthermore, there is a commercial library of tools that use the SMILES notation to support sub/superstructure searches and other connectivity relatedness searches. The developer of SMILES also developed a thesaurus-oriented database ('THOR') which stores, on a per chemical basis, any type of information that you care to store (the fields are user-definable). The keys to records are SMILES notation representations of the chemicals. The company is: DAYLIGHT CIS P.O. Box 17821 Irvine, CA USA 92713-7821 (714) 586-6927 (714) 476-0451 I also know a bit about the Cambridge Structural Database in which you can do substructure searches. Encoded in the CSD are bitmaps representing the presence or absense of properties that are the basis rapidly eliminating a large number of candidates during searches. I imagine many other chemical databases are concerned with properties of chemicals. But my interest is also in the relationships between properties since that is the basis of a taxonomy. So this is an open invitation to keep me informed of any relevant information on this subject that you may come across, and I will summarize periodically for this list. Thanks. liberte@ncsa.uiuc.edu (217) 244-0785 Daniel LaLiberte National Center for Supercomputing Applications 152 Computing Appliations Building 605 East Springfield Avenue Champaign, IL 61820 From chemistry-request@ccl.net Thu Jul 11 20:39:25 1991 Date: Thu, 11 Jul 91 20:29:29 -0400 From: neal@charles.polymer.uakron.edu (Neal Neuburger) To: chemistry@ccl.net Subject: Crystal Structure of Quartz Status: R I am trying to build a quartz crystal to be used in analyzing a polymer quartz interface. Does anyone have a machine readable structure file. Or any information on the crystal structure of quartz, i. e., the space group and lattice dimensions. The reference that I am currently using is: Crystal Structures, Vol. 1, R.W.G. Wickoff, Wiley Interscience, P312. The above reference seems to be in error with the respect the the Space group. They say that the space group is P312 and then say that it is a hexagonal structure. P312 is a trigonal space group. Neal Neuburger From chemistry-request@ccl.net Thu Jul 11 23:12:31 1991 Date: Thu, 11 Jul 91 22:40:58 EDT From: states@ncbi.nlm.nih.gov (David States) To: chemistry@ccl.net, liberte@ncsa.uiuc.edu Subject: Re: Chemistry Taxonomy Status: R Daniel LaLiberte (liberte@ncsa.uiuc.edu) writes: I had asked in May for information on chemistry taxonomies, especially related to object-oriented classification of chemistry concepts.... Which raises the question: do you really want a taxonomy, or would you in fact want an efficient subgraph matching and lookup algorithm? A taxonomy implies a statitic, hierarchical classification of the data, but different users of a chemical database almost certainly have different applications and different views in mind. In building a literature retrieval tool, we have found that local neighboring is a very useful approach. Instead of trying to organize the whole database by one criterion, a network of nearest neighbors is built based on a distance measure. For bibliographic citations, this measure is based on similarity of vocabulary use, authors etc., but for chemical structure, it could be based on subgraph matching of structures. Access to the database is done by starting with an initial entry and "exploring" nearest neighbors to wander through the network. Users seem to find this approach to be natural and powerful. The CarbBank (carbohydrate database) group at the University of Georgia has done some interesting work with those approach applied to looking up complex carbohydrate structures. Contact carbbank@uga.bitnet for additional information. David States National Center for Biotechnology Information / National Library of Medicine From chemistry-request@ccl.net Thu Jul 11 23:31:28 1991 Date: Thu, 11 Jul 1991 23:12:58 EDT From: bell@XRAY.CHEM.RPI.EDU To: chemistry@ccl.net Subject: Modeling Workshop at Rensselaer Status: R Deadline for application to the Molecular Modeling Workshop at Rensselaer Polytechnic Institute is almost here. You still have time to send an application by E-mail or FAX. If you need a workshop brochure, I will E-mail a copy to you on request. Hint for you procrastinators (like me): Applications that reach the committee by Monday morning will probably still be considered. Those who have already applied will receive a reply via E-mail or phone by Monday, July 15, at the latest. Additional guest lecturer not mentioned in the brochure will be DeLos DeTar, Florida State University. Jeffrey Bell bell@xray.chem.rpi.edu