From cathy@judith.saclay.cea.fr Wed Jan 19 05:51:18 1994 Received: from pamir.inria.fr for cathy@judith.saclay.cea.fr by www.ccl.net (8.6.4/930601.1506) id FAA14220; Wed, 19 Jan 1994 05:01:18 -0500 X400-Received: by /PRMD=inria/ADMD=atlas/C=fr/; Relayed; 19 Jan 94 11:01:16+0100 X400-Received: by /PRMD=cea/ADMD=atlas/C=FR/; Relayed; 19 Jan 94 15:52:30+0000 Date: 19 Jan 94 15:52:30+0000 From: Catherine TENETTE Message-ID: <9401191000.AA27746@oeillet.saclay.cea.fr> Subject: protein structure To: chemistry@ccl.net Mailer: Elm [revision: 70.85] Hi! I'm working on protein structure and I'm looking for a program which could determine the relative orientation of two close packed beta sheets. Send me every idea or program you could have. Thank you for replying over the net. From szeinfel@fox.cce.usp.br Wed Jan 19 07:51:23 1994 Received: from bee08.uspnet.usp.br for szeinfel@fox.cce.usp.br by www.ccl.net (8.6.4/930601.1506) id HAA14780; Wed, 19 Jan 1994 07:31:33 -0500 Received: from fox.cce.usp.br (fox.cce.usp.br [143.107.70.1]) by bee08.uspnet.usp.br (8.6.4/RISC-CCE2.0) id KAA28965 Received: from localhost (szeinfel@localhost) by fox.cce.usp.br (8.6.4/CONVEX120-CCE2.0) id KAA01710 Date: Wed, 19 Jan 1994 10:25:07 -0300 (BST) From: Rafael N Szeinfeld Subject: Re: protein structure To: Catherine TENETTE cc: chemistry@ccl.net In-Reply-To: <9401191000.AA27746@oeillet.saclay.cea.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On 19 Jan 1994, Catherine TENETTE wrote: > Hi! > I'm working on protein structure and I'm looking for a program which > could determine the relative orientation of two close packed beta sheets. > Send me every idea or program you could have. > Thank you for replying over the net. > Hi Catherine, What kind of data you want & have to give the program as input ? Sincerly yours, Rafael Najmanovich From grzesb@asp.biogeo.uw.edu.pl Wed Jan 19 08:51:25 1994 Received: from asp.biogeo.uw.edu.pl for grzesb@asp.biogeo.uw.edu.pl by www.ccl.net (8.6.4/930601.1506) id IAA14990; Wed, 19 Jan 1994 08:01:05 -0500 Received: by asp.biogeo.uw.edu.pl (5.61/1.34) id AA24528; Wed, 19 Jan 94 11:53:24 +0100 Date: Wed, 19 Jan 94 11:53:24 +0100 From: grzesb@asp.biogeo.uw.edu.pl (Grzegorz Bakalarski) Message-Id: <9401191053.AA24528@asp.biogeo.uw.edu.pl> To: chemistry@ccl.net Subject: Summary: semiempirical DFT Organization: Dept. of Biophys., Warsaw Univ. Poland Cc: grzesb@asp.biogeo.uw.edu.pl Dear Netters, A few days ago I have asked CCL users about SEMIEMPIRICAL DFT methods. These are replies I have got until now. I think this is enough to start dealing with the problem. THANKS TO ALL OF YOU WHO HAVE REPLIED. Thanks a lot. Best regards to all of you CCL Netters Grzegorz Bakalarski ORIGINAL QUERRY: ^^^^^^^^^^^^^^^ Dear Netters, I am interested in semiempirical DFT. Do you know (or have you heard) about such approach ? Semiepirical DFT is (or maybe '' would be'') a method similar to semiempirical method in QM ( like MNDO, INDO etc.) but instead of wave function it uses density (or maybe monopoles,dipoles quadrupoles etc. of density or density matrix coefficients) and some empirical coefficient. ANY ARTICLE - CONTACT - or other informations are welcomed. I will summarize if there is any interest in this topic . Grzegorz Bakalarski REPLIES: ^^^^^^^^ ********************************************* From: bohrf@CHIMCN.UMontreal.CA (Bohr Frederic) Subject: Re: semiempirical DFT Dear Dr Bakalarski, In the book of R.G. Parr and W. Yang about Density-Functional Theory, there is a little part concerning the semiempirical DFT in which some references are given. In my opinion, those which could be interesting for you are: - E. Lindholm and L. Asbrink (1985). Molecular Orbitals and their Energies, studied by the Semiempirical HAM Method. Berlin: Springer- Verlag. - E. Lindholm and S. Lundqvist (1985). Semiempirical MO methods, deduced from density functional theory. Phys. Scr. 32: 220-224. I give you also the reference of the Parr and Yang's book for other references: - R.G. Parr and W. Yang (1989). Density Functional Theory of Atoms and Molecules. Oxford Univ. Press, New York. I hope I have helped you. Frederic Bohr (bohrf@CHIMCN.UMontreal.CA) ************************************************* This mail is in Polish.(I have translated it to English. [Sorry Piotr for may English] ) Dr P. Rozyczko says: (in brief) DFT is from the beginning semiempirical. It manifest in correlation-exchange potential which is usually fitted to experiment (It does not come from first principles). An apparent simplification may cause in incorrect description of a system. Original message: From: "Piotr B Rozyczko" Subject: Re: semiempirical dft Density Functional Theory w wydaniu polempirycznym? Przeciez z zalozenia DFT jest parametryzowane empirycznie. W teorii DFT staramy sie znalezc (niekiedy tak ad hoc, z powietrza!) pewien potencjal, opisujacy interesujace nas zjawisko czy uklad. Owo wyrazenie na potencjal dopasowywujemy do wynikow doswiadczalnych poprzez wlasnie szereg parametrow, tak aby oddawalo eksperyment z jak najmniejszym bledem. Zas pozorne uproszczenie obliczen poprzez szybkie liczenie macierzy gestosci spowodowac _moze_ (chyba nikt tego jeszcze nie robil) nieprawidlowy opis ukladu czy zjawiska, nie do poprawienia przez parametryzacje. Jest to moj prywatny poglad, jesli istnieja jednak jakies ciekawe przyklady uzycia przyblizenia ZDO do modelowania potencjalow DFT, bardzo chetnie o nich uslysze. Z powazaniem, Piotr Rozyczko Quantum Theory Project rozyczko@qtp.ufl.edu ****************************************************** From: Dr. Rene Fournier Subject: semi-empirical DFT methods. Hi ; There is a family of methods based on the embedded atom, some of which may be called semi-empirical. The starting point of these methods is the interaction energy (calculated from first-principles) of an atom and a homogeneous electron gas. From there on, many variants are possible. Good references on these methods are: 1- T. J. Raeker and A. E. DePristo, Int. Rev. Phys. Chem. 10, 1 (1991) and articles cited in it : First-principles calculations of embedded atoms : 2- M. J. Puska, R. M. Nieminen, and M. Manninen, Phys. Rev. B 24, 3037 (1981) Effective Medium (EM) theory : 3- M. J. Stott and E. Zaremba, Phys. Rev. B 22, 1564 (1980) 4- J. K. Norskov and N. D. Lang, Phys. Rev. B 21, 2131 (1980) 5- K. W. Jacobsen, J. K. Norskov, and M. J. Puska, Phys. Rev. B 35, 7523 (1987). 6- K. W. Jacobsen, J. K. Norskov, Phys. Rev. Lett. 59, 2764 (1987) 7- K. W. Jacobsen, J. K. Norskov, Phys. Rev. Lett. 60, 2496 (1988) 8- K. W. Jacobsen, Comments Condens. Matter Phys. 14, 129 (1988) Corrected Effective Medium (CEM): 9- J. D. Kress and A. E. DePristo, J. Chem. Phys. 87, 4700 (1987) 10- J. D. Kress and A. E. DePristo, J. Chem. Phys. 88, 2596 (1988) 11- J. D. Kress, M. S. Stave, A. E. DePristo, J. Phys. Chem. 93, 1556 (1989) 12- T. J. Raeker and A. E. DePristo, Phys. Rev. B 39, 9967 (1989) 13- M. S. Stave, D. E. Sanders, T. J. Raeker, and A. E. DePristo, J. Chem. Phys. 93, 4413 (1990) Embedded Atom Model (EAM) 14- M. S. Daw, M. I. Baskes, Phys. Rev. B 29, 6443 (1984) "glue" model : 15- F. Ercolessi, M. Parrinello, and E. Tosatti, Surf. Sci. 177, 314 (1986) Finnis-Sinclair model : 16- M. W. Finnis, J. E. Sinclair, Philos. Mag. A 50, 45 (1984). There is a brief discussion, and references, on semi-empirical DFT models completely different from the above in section 10.6 of : R. G. Parr and W. Yang, "Density-Functional Theory of Atoms and Molecules", (Oxford University Press, New York, 1989) I'm interested in knowing more about semi-empirical DFT methods, please send a summary of answers to OSC list or to my e-mail. Thanks. ******************************************************************* From: scsupham@reading.ac.uk Subject: Re: semiempirical dft Hi, I would be interested in any replies you receive. Normal DFT is relatively efficient anyway because the scaling factor (N^3 as the number of basis functions) is not high. I`m not sure there is a great demand for semi-empirical DFT. How would you parameterise it - on other ab initio calcs or on expt ?? best wishes, john upham END of FILE ^^^^^^^^^^^ From richard@iris26.biosym.com Wed Jan 19 12:51:33 1994 Received: from bioc1.biosym.com for richard@iris26.biosym.com by www.ccl.net (8.6.4/930601.1506) id MAA17905; Wed, 19 Jan 1994 12:42:26 -0500 Received: from iris26.biosym.com by bioc1.biosym.com (5.64/0.0) id AA07543; Wed, 19 Jan 94 09:41:54 -0800 Received: by iris26.biosym.com via SMTP (931110.SGI.ANONFTP/920502.SGI) for @bioc1.biosym.com:chemistry@ccl.net id AA28656; Wed, 19 Jan 94 09:41:43 -0800 Message-Id: <9401191741.AA28656@iris26.biosym.com> To: Catherine TENETTE Cc: chemistry@ccl.net, richard@iris26.biosym.com Subject: Re: protein structure In-Reply-To: Your message of "19 Jan 94 15:52:30 GMT." <9401191000.AA27746@oeillet.saclay.cea.fr> Date: Wed, 19 Jan 94 09:41:42 -0800 From: Richard Macdonald > Mailer: Elm [revision: 70.85] > Sender: chemistry-request@ccl.net > Errors-To: jkl@ccl.net > Precedence: bulk > > Hi! > I'm working on protein structure and I'm looking for a program which > could determine the relative orientation of two close packed beta sheets. > Send me every idea or program you could have. > Thank you for replying over the net. > > > > ---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 (port 70 or 73) > Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search DON'T TELL THEM ABOUT MOMENT OF INERTIA TENSOR!!! -----> richard From h.rzepa@ic.ac.uk Wed Jan 19 13:51:23 1994 Received: from punch.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.4/930601.1506) id NAA18172; Wed, 19 Jan 1994 13:05:36 -0500 Received: from sg1.cc.ic.ac.uk by punch.ic.ac.uk with SMTP (PP) id <05504-0@punch.ic.ac.uk>; Wed, 19 Jan 1994 18:02:22 +0000 Received: from macb.ch by cscmgb.cc.ic.ac.uk (920330.SGI/4.0) id AA07546; Wed, 19 Jan 94 18:04:00 GMT Message-Id: <9401191804.AA07546@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: Wed, 19 Jan 1994 18:05:22 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: www, gopher and others. What every chemist should know! >But when you begin to write about mosaic, www, http, html+, etc, I am in >trouble and I am sure I am not the only one : can you explain in a few >words what these things are ? I suppose other readers of the watoc list or >the computational chemistry list would also appreciate such a glossary. Following the above request, here is a brief potted summary of these tools. For those of you who are already using them, please ignore. Gopher. A server program for a distributed database of files, containing useful information, not only locally, but with pointers to other useful sites. The server normally runs on a Unix workstation, but can in fact also run happily on a Mac (and probably PC). It provides to end users not only text files, but binary files (ie programs) or documents (eg MS Word), pictures (ie gif or pict). A new version called gopher+ also serves up eg video (ie quicktime or mpeg), sounds (ie ulaw) and other types of files. Few gophers are yet up to + standard. Our gopher+ is gopher.ch.ic.ac.uk. To connect, use a client program and make sure your computer is connected to the internet, with an assigned IP address. This can be done with an ethernet card and eg PC-NFS 5.0B (for PC), or MacTCP 2.04. You can also do this from home. On a Mac, I use MacTCP 2.04, another program called MacPPP 2.02 and a 14.4K modem, connecting to a "PPP" server. In my case, this is an Annex server connected to our institutional ethernet. The client program on a Mac is called Turbogopher. The interface is designed to be as easy as pssible to use. You click on the file and over it comes. On a PC it is called hGopher, on Unix XGopher. You may also need "helper programs", ie viewers for the images, or the movies or sounds. Gopher will help you find this. World-wide-Webb. A Hypermedia based system. Basically, the same types of files as above, but where the cross referencing links are done within the files themselves, rather than at the server level. Uses a script called "html". Anyone who is familiar with eg MTROFF or early non WYSIWYG word processors will feel at home! To connect, get a "Browser" such as NCSAMosaic (availble for PC, Mac and Unix). Feed it a "URL" such as the one below. Some text will be highlighted, which means you can click on it to get something more (ie more text, pictures, sounds etc). The cross references mean you can start off on one topic and end up somewhere else. This is what distinguishes it from gophers. For example, the new Hubble space pictures were made available within hours of being processed! To author material using www requires some tools, ie write what you want in eg MS Word, including all diagrams etc, save as an rtf file, and then use a program called rtf2html to convert to html. Mount this in a specified directory on the www server. The latter is again normally Unix, but can quite safely be eg a Mac. html+. Raw html is not quite suitable for chemists, ie no greek letters, no superscripts, tables etc. html+ is supposed to address all these issues, but it is not available yet. There is much I have missed out, but I hope this helps. PS Hundreds of requests for all this software will not be answered by me. Sorry! I could not cope. Get it using Mosaic from NCSA themselves. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 2.01, Tel:+44 71 225 8339, Fax:+44 71 589 3869. >From June '94: (44) 171 584 5774, Fax: (44) 171 584 5804 http://www.ch.ic.ac.uk/rzepa.html From bkarlak@ren.onyx-pharm.com Wed Jan 19 14:51:24 1994 Received: from iserver.onyx-pharm.com for bkarlak@ren.onyx-pharm.com by www.ccl.net (8.6.4/930601.1506) id OAA18906; Wed, 19 Jan 1994 14:35:32 -0500 Received: from ren.onyx-pharm.com by iserver.onyx-pharm.com (5.67/1.37) id AA26163; Wed, 19 Jan 94 11:35:26 -0800 Received: by ren.onyx-pharm.com (920330.SGI/921111.SGI.AUTO) for @iserver.onyx-pharm.com:chemistry@ccl.net id AA05780; Wed, 19 Jan 94 11:35:53 -0800 Date: Wed, 19 Jan 94 11:35:53 -0800 From: bkarlak@ren.onyx-pharm.com (Brian Karlak) Message-Id: <9401191935.AA05780@ren.onyx-pharm.com> To: chemistry@ccl.net Subject: OK - fess up. OK, Richard - now you get to explain that oh-so-cryptic comment about inertia tensors to the rest of us . . . Brian This signature file intentionally left blank. From carolyn@emx.cc.utexas.edu Wed Jan 19 14:59:08 1994 Received: from emx.cc.utexas.edu for carolyn@emx.cc.utexas.edu by www.ccl.net (8.6.4/930601.1506) id OAA18874; Wed, 19 Jan 1994 14:31:57 -0500 Received: from [128.83.142.17] (mac7.lanic.utexas.edu [128.83.142.17]) by emx.cc.utexas.edu (8.6.4/8.6.4/emx-1.1) with SMTP id KAA05336 for ; Wed, 19 Jan 1994 10:25:17 -0600 Date: Wed, 19 Jan 1994 10:25:17 -0600 Message-Id: <199401191625.KAA05336@emx.cc.utexas.edu> To: chemistry@ccl.net From: carolyn@emx.cc.utexas.edu (Carolyn Poage) X-Sender: carolyn@emx.cc.utexas.edu Subject: Electronic Databases Greetings: We would like to know what electronically available databases you are using in your field. The Institute of Latin American Studies (ILAS), University of Texas at Austin, has developed a directory of information publically available on the Internet called the Latin American Network Information Center (UT-LANIC). UT-LANIC objectives are to provide Latin American and all other users with access to academic databases and information services worldwide, and to provide Latin Americanists around the world with access to information on and from Latin America. We want to expand the listings in the sciences. Can you suggest on-line databases to be added to the directory? We are very interested to hear what you are using in your field of expertise. Helpful information would be the name of the database, the host name, and the type of access. If you have direct access to the Internet, we'd like to invite you to access UT-LANIC. To access UT-LANIC if you have a gopher client, please type gopher lanic.utexas.edu If you have to telnet to it, type telnet lanic.utexas.edu login: lanic After a moment, you will see UT-LANIC top-level menu. Following the instructions on the screen, you can check the information you need. Features of UT-LANIC are: - Directory of databases by subject - Databases automatically accessed through pointers--not dialing - All subjects covered, but only the most valuable databases in each - Quick reference and up front evaluation of databases - Host for Latin American databases - Public domain (free of charge) We appreciate your input! Carolyn Poage Palaima carolyn@emx.cc.utexas.edu Institute of Latin American Studies University of Texas at Austin From burke@agouron.agouron.com Wed Jan 19 15:51:25 1994 Received: from agouron.com for burke@agouron.agouron.com by www.ccl.net (8.6.4/930601.1506) id PAA19447; Wed, 19 Jan 1994 15:39:48 -0500 Received: from agouron.agouron.com by agouron.com via SMTP (931110.SGI.ANONFTP/931108.SGI.AUTO.ANONFTP) for chemistry@ccl.net id AA25962; Wed, 19 Jan 94 12:41:28 -0800 Received: by agouron (5.64/10.0) id AA14039; Wed, 19 Jan 94 12:41:26 -0800 Date: Wed, 19 Jan 94 12:41:26 -0800 From: burke@tbone.agouron.com (Ben Burke) Message-Id: <9401192041.AA14039@agouron> To: chemistry@ccl.net Subject: radial distribution function factor Hello CCL-ers, I'm posting this question for a friend: Integration of the radial distribution function to obtain a coordination number seems to require a conversion factor: 1000 r^2 -------- k * T^2 where r = distance, k= Boltzmann's constant, and T is temperature. Can anyone explain where this factor comes from and why it is needed to obtain a coordination number? Thanks, Ben Burke burke@agouron.com From richard@iris26.biosym.com Wed Jan 19 16:51:30 1994 Received: from bioc1.biosym.com for richard@iris26.biosym.com by www.ccl.net (8.6.4/930601.1506) id QAA19893; Wed, 19 Jan 1994 16:29:05 -0500 Received: from iris26.biosym.com by bioc1.biosym.com (5.64/0.0) id AA10799; Wed, 19 Jan 94 13:28:34 -0800 Received: by iris26.biosym.com via SMTP (931110.SGI.ANONFTP/920502.SGI) for @bioc1.biosym.com:chemistry@ccl.net id AA28991; Wed, 19 Jan 94 13:28:29 -0800 Message-Id: <9401192128.AA28991@iris26.biosym.com> To: bkarlak@ren.onyx-pharm.com (Brian Karlak) Cc: chemistry@ccl.net, richard@iris26.biosym.com Subject: Re: OK - fess up. In-Reply-To: Your message of "Wed, 19 Jan 94 11:35:53 PST." <9401191935.AA05780@ren.onyx-pharm.com> Date: Wed, 19 Jan 94 13:28:28 -0800 From: Richard Macdonald Precedence: bulk > > > OK, Richard - now you get to explain that oh-so-cryptic comment about inertia > tensors to the rest of us . . . > > Brian > I guess you're right! I already apologized to the person who posted the original request directly. I meant the message to go to Mark Forster here who is working on moment of inertia tensors. By mistake I pressed the Send button before I edited the address! I guess this happens to everyone at least once in their lifetimes... Mark and I are going to try using the moment of inertia tensors to align structural motifs, but we didn't intend to broadcast this idea yet! This faut paux will go down in my personal history as one of those never-forgotten events.... Anyway, since now you know, is it a good idea? -----> richard *********************************************************** Richard D. Macdonald, Ph.D. voice: (619) 546-5527 Lead Scientist Biosym Technologies internet: richard@biosym.com 9685 Scranton Road San Diego, CA 92121-2777 ***********************************************************