From chemistry-request@www.ccl.net Wed Sep 23 03:26:28 1998 Received: from hpserv.imim.es ([193.144.6.104]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA25984 Wed, 23 Sep 1998 03:26:26 -0400 (EDT) Received: from i25.imim.es ([193.144.6.234]) by hpserv.imim.es with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.1960.3) id SN0KRG20; Wed, 23 Sep 1998 09:24:34 +0100 Message-ID: <3608A289.C78A6D2F@imim.es> Date: Wed, 23 Sep 1998 09:26:01 +0200 From: "Jordi Villŕ" X-Mailer: Mozilla 4.01 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: MEPSIM 2.4 X-Priority: 3 (Normal) Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit MEPSIM (http://www1.imim.es/~mepsim/index.htm) is a computational system developed by the Department of Medical Computer Sciences of the Institut Municipal d'Investigació Mčdica of Barcelona.(1) It permits an integrated computation and analysis of the Molecular Electrostatic Potential (MEP). It includes the following main modules: MEPMIN: A module which allows to find automatically the MEP minima of a molecular system. It supplies the cartesian coordinates of these minima, their values and all the geometrical relationships between them (distances, angles and dihedral angles). This module uses the exact definition of MEP.(2) MEPCOMP: This module computes a similarity coefficient between the MEP distributions of two molecules and finds their relative position that maximizes this electrostatic similarity.(3,4) In MEPSIM 2.4 there is a new utility that allows the comparison of the whole MEP distributions of two molecules or only their negative zones.(5) The second option avoids the influence of the nuclear positive MEP zones in the comparison. In this option the user can define the MEP value that limits the negative MEP zones to be considered. An earlier version of MEPSIM, that was programmed to run on a VAX system, included other modules. The migration of VAX systems to UNIX workstations in many research laboratories, made convenient to develop a new version of the MEPSIM package that runs on UNIX SGI machines. Nevertheless some options of the package have not yet been completely developed for UNIX SGI systems, so they are not available in this new version of MEPSIM. On the other side, the capabilities of the available modules in terms of maximum number of atoms and orbitals, have been increased. 1.Sanz F, Manaut F, Rodriguez J, Lozoya E, and López-de-Brinas E, MEPSIM: A computational package for analysis and comparison of moleculra electrostatic potentials. J. Comput.-Aided Mol. Design, 7(1993)337. 2.Sanz F, Manaut F, José J, Segura J, Carbó M and De-la-Torre R, Automatic determination of MEP patterns of molecules and its application to cafeine metabolism inhibitors. J. Mol. Struct. (Theochem) 170(1988)171. 3.Sanz F, Manaut F, José J and Milesi M, Automatic search for maximun similarity between molecular electrostatic potential distributions. J. Comput.-Aided Mol. Design, 5(1991)371. 4.Manaut F, Lozoya E and Sanz F, Automatic determination of maximun electrostatic alingment between methotrexate and dihydrofolic acid. In Silipo,C. and Victoria, A. (Eds) QSAR: Rational Aproaches to the Design of Bioactive Compounds, Elsevier, Amsterdam, 1991, pp. 339-342. 5.Lozoya E, Berges M, Rodriguez J, Sanz F, Loza MI, Moldes VM, Masaguer CF Comparison of electrostatic similarity approaches applied to a series of ketanserin analogues with 5-HT2A antagonistic activity. Quant Struc-Act Relat, 17(1998)199. -- Jordi Villŕ Research Group on Medical Informatics Carrer del Doctor Aiguader 80 E-08003 Barcelona Tlf: 34-93-2211009 Fax: 34-93-2213237 jvilla@imim.es From chemistry-request@www.ccl.net Thu Sep 24 10:05:31 1998 Received: from schubert.ciam.unibo.it (schubert.ciam.unibo.it [137.204.214.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA13236 Thu, 24 Sep 1998 10:05:29 -0400 (EDT) Received: by schubert.ciam.unibo.it; id AA02902; Thu, 24 Sep 1998 16:10:26 GMT Sender: igor@schubert.ciam.unibo.it Message-Id: <360A6EF1.41C6@schubert.ciam.unibo.it> Date: Thu, 24 Sep 1998 16:10:25 +0000 From: Igor Mumelter Organization: University of Bologna - Chemistry Department X-Mailer: Mozilla 3.01Gold (X11; I; OSF1 V4.0 alpha) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: RR spectra of metallo porphyrines Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Status: RO Content-Length: 817 Dear CCL'ers, could anybody give me some references about experimental resonance Raman spectra of free base porphyrine and his magnesium and zinc derivatives? Any hints would be greatly appreciated. Please reply to the list and to my personal e-mail address at: igor@schubert.ciam.unibo.it Best regards and thanks in advance Igor "480K should suffice to anyone" (Bill Gates) *********************************************************************** Dr. Igor Mumelter Ph.D. Student in Computational Chemistry Dip. di Chimica "G.Ciamician" via Selmi 2 I-40126 Bologna Italy e-mail:igor@schubert.ciam.unibo.it phone: +39 51 259498, fax -56 Italian Ph.D. Association (ADI) ADI-Bologna http://welcome.to/adi *********************************************************************** From chemistry-request@www.ccl.net Wed Sep 23 03:46:26 1998 Received: from apollon.bender.co.at (apollon.bender.co.at [193.154.107.33]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA26058 Wed, 23 Sep 1998 03:46:22 -0400 (EDT) Received: from vieexch1.vie.at.bic (vieexch1 [148.190.11.2]) by apollon.bender.co.at (8.9.1/8.6.9) with ESMTP id JAA00204 for ; Wed, 23 Sep 1998 09:46:19 +0200 Received: by vieexch1.vie.at.bic with Internet Mail Service (5.5.1960.3) id ; Wed, 23 Sep 1998 09:39:59 +0200 Message-ID: <4195A3C6D39BD11189C30020AFFC17588F3BD9@vieexch1.vie.at.bic> From: "LOEFFLER,DR,GERALD FEM BENAT" To: chemistry@www.ccl.net Subject: RE: CASP vs. The Tower of Babel Date: Wed, 23 Sep 1998 09:39:58 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Hi! So why is there no collaboration on the code-level between computational scientists? I don't want to over-simplify the problem, but one important reason IMHO is the fact that traditionally computational scientists have been _lousy_ programmers. While the technology to make interoperable application components has been there for some time (I'm particularly thinking of OO technology), computational scientists have been too inexperienced in software engineering techniques to exploit this technology. As a concrete example: It would be almost trivial to design an OO framework for Energy Minimization (or Molecular Dynamics or Threading, ...) where the force-field would be just one component that you "plug" into the framework. The same is true for such algorithmic components as minimization strategies, potentials of mean force, integration algorithms, Monte Carlo moves, Genetic Algorithms, etc. But is the resulting code efficient? It's certainly a lot slower than FORTRAN! (For language reasons and because you loose opportunities for source-level optimizations if components have to be truly independent of each other.) But I would argue that firstly speed of execution does not matter at this level (we are not talking about production code here). And secondly, on the other hand, of what use is speed of execution if you can not get the functionality you want (interoperability of algorithms, in this case) with reasonable effort? But things _are_ getting better: MMTK springs to my mind, and also the OMG effort to standardize interfaces for biological sequence analysis (although this is not an academic effort). And of course there are programs which are not designed with OO techniques and consequent interoperability in mind, but which are simply well written (TINKER, for instance). (Regarding unwillingness to give away source code at all: With Java you can even give away the "object code" (byte code) (maybe after running it through an obfuscator) and it will work on any Java platform...) cheers, gerald |--------------------------------------------------------------------| Gerald Loeffler - Bioinformatics Scientist Boehringer Ingelheim R&D Vienna Email: Gerald.Loeffler@vienna.at Phone: +43 676 3289588 (and +43 1 80105 634) Fax: +43 1 80105 683 Smail: Bender+Co, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria > -----Original Message----- > From: Gabriel Berriz [SMTP:berriz@potato.harvard.edu] > Sent: Sunday, September 20, 1998 7:53 PM > To: chemistry@www.ccl.net > Subject: CCL:CASP vs. The Tower of Babel > > > > I study the statistical mechanics of protein folding using minimal > computer models. I find that my specialty has a Tower of Babel > (Babble?) problem, and perhaps the same is true of the whole field of > computational protein studies, or even of all of computational > chemistry. It has to do with checking and building on the results of > others. I was an experimentalist in cellular immunology for a few > years before switching to my current field, and I recall that trading > reagents, libraries, strains, was quite common in that field. I often > unpacked little vials shipped in dry ice, and bearing some precious > mutant; typically, after some quick tests, I was up and running with > the new stuff. Not much was required from the source of the samples > (a couple of concentrations, buffers used, maybe some growth > conditions here and there...). > > *Nothing* like this happens in my current field. I'm not sure why, > but I have a few guesses. For one thing, programs are a pain to port > across systems (portability of code is not a criterion for > publication). More important, in most cases I don't want the program > just to use as a black box. On the contrary, my interest in the > program is usually in how it implements a model; I want not only to > reproduce published results, but also to tweak the conditions, and to > extend the experiments. This invariably requires that I understand > enough of the code to hack away in it, and here's where I hit the > biggest wall. It takes me too long to understand the code written by > my *labmates*, let alone that written by some unknown graduate student > 5 years ago half a world away. (Again, clarity of code is, for the > most part, not a criterion for publication). So, typically I conclude > that either I re-implement the idea from scratch, which is usually > something I can't afford, or else I drop the matter altogether. > (Incidentally, in the few cases I've tried to get source code from > other labs, I've received such unequivocal, resounding, unapologetic > refusals, that I must conclude my request was deemed to be bad > manners.) > > It is, in my opinion, a very serious problem; it reduces the field to > a collection of largely independent efforts, deprived of one of the > greatest strengths of the scientific method, namely, the ability to > test and build upon the work of others. I wonder if others feel > similarly. > > I think this frustrating situation was what ultimately gave rise to > the biennial structure prediction competition CASP (Critical > Assessment of techniques for protein Structure Prediction), in which > participants put their structure prediction programs through the fire > test of predicting some recently solved protein structures prior to > their publication. This skips over the problem of understanding the > programs and the models devised by others by focusing on "objective > results". Faced with this clear prize, the field has naturally > responded by a adopting an increasingly heuristic attitude: whatever > works, however ad hoc or poorly understood, throw it in there. If you > loose, no one will care, and if you hit the CASP jackpot, then > "there's no arguing with success!" > > Well, I guess that's *one* way to deal with our Tower of Babel > problem, but I wonder where this leaves the science... I'm relatively > new to this field, though, and I wonder what others with more > experience feel about these issues. > > Best wishes, > > Gabriel Berriz > Department of Chemistry and Chemical Biology > Harvard University > berriz@potato.harvard.edu > For best results, replace the word potato by chasma in my address. > > > --- > Administrivia: This message is automatically appended by the mail > exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: > Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: > www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive > search > Web: http://www.ccl.net/chemistry.html > --- From chemistry-request@www.ccl.net Thu Sep 24 14:36:56 1998 Received: from alpha2.albany.edu (SYSTEM@alpha2.cnsvax.albany.edu [169.226.1.27]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA01667 Thu, 24 Sep 1998 14:36:54 -0400 (EDT) Received: from ch3f153.chem.albany.edu ([169.226.115.200]) by cnsvax.albany.edu (PMDF V5.1-12 #18385) with SMTP id <01J26SE61OV88X23IG@cnsvax.albany.edu> for chemistry@www.ccl.net; Thu, 24 Sep 1998 14:39:28 EDT Date: Thu, 24 Sep 1998 14:36:51 +0000 From: Rolf Claessen Subject: Re: CCL:books for theor.chem. In-reply-to: <199809231236.OAA15662@rs5.thch.uni-bonn.de> To: Bernd Engels , chemistry@www.ccl.net Reply-to: rc7980@cnsvax.albany.edu Message-id: <01J26SE622ZQ8X23IG@cnsvax.albany.edu> Organization: Claessen.Net MIME-version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Priority: normal Status: RO Content-Length: 339 Hi Bernd, I have listed quite a view books at http://www.claessen.net/chemistry/book_en.htm some with reviews. Gruss aus Albany, Rolf ___________________________ Rolf Claessen Chemistry Department SUNYA Albany NY 12222 USA Tel. US - 518 - 442 - 4444 Fax US - 518 - 442 - 3462 Email rolf@claessen.net WWW http://www.claessen.net From chemistry-request@www.ccl.net Wed Sep 23 08:36:29 1998 Received: from rs5.thch.uni-bonn.de (rs5.thch.uni-bonn.de [131.220.44.15]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA26988 Wed, 23 Sep 1998 08:36:26 -0400 (EDT) Received: (from bernd@localhost) by rs5.thch.uni-bonn.de (8.8.8/8.8.5) id OAA15662 for chemistry@www.ccl.net; Wed, 23 Sep 1998 14:36:54 +0200 From: Bernd Engels Message-Id: <199809231236.OAA15662@rs5.thch.uni-bonn.de> Subject: books for theor.chem. To: chemistry@www.ccl.net (Computational Chemistry List) Date: Wed, 23 Sep 1998 14:36:53 +0200 (MES) Hy, I would be interested in an overview about good books about Theoretical Chemistry. I am mainly interested in books for undergraduate students but other comments are also highly appreciated. Of course I will summarize Bernd Engels Inst. fuer Phys. und Theor. Chemie Universitaet Bonn Germany From chemistry-request@www.ccl.net Thu Sep 24 19:25:08 1998 Received: from blucher.qf.ub.es (blucher.qf.ub.es [161.116.73.138]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA24973 Thu, 24 Sep 1998 19:25:04 -0400 (EDT) Received: from payes (payes.red.retevision.es [62.81.62.7]) by blucher.qf.ub.es (8.8.5/8.8.5) with SMTP id BAA21792; Fri, 25 Sep 1998 01:14:23 +0200 Message-ID: <199809250124400523.10D9ECC0@blucher.qf.ub.es> In-Reply-To: References: X-Mailer: Calypso Version 2.40.40 Date: Fri, 25 Sep 1998 01:24:40 +0200 From: "Juan Miguel Bocanegra" To: abjones@nmsu.edu, chemistry@www.ccl.net Subject: Re: CCL:Contour Plots Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id TAA24974 Status: RO Content-Length: 1239 Abraham, On 24/9/98, at 22:31, Abraham Jones wrote: >Hello, > > Greetings from NM. I found your address on the internet when I search >for help on generating contour plots with Gnuplot . I'm trying to >generate some 2-D contour plots and I can't get it to work. Gnuplot >always says that it can't contour non-grid data. I have my data files >set up with three columns x,y & z. I had the same problem some days ago. I also thought gnuplot was capable of plotting contours from a 'standar' collection of x,y,z coordinates. This is wrong IMHO, as far as I've seen (x,y) pairs _need_ form a grid, i.e, your data file must have the form x1 y1 z(x1,y1) x1 y2 z(x1,y2) ... x1 yn z(x1,yn) # blank line x2 y1 z(x2,y1) x2 y2 z(x2,y2) ... x2 yn z(x2,yn) and so on. Hope this helps, anyway look at the manual coming with the distribution. JM LIFE IS SO UNCERTAIN - EAT DESSERT FIRST Juan Miguel Bocanegra Moron (mailto:juanmi@blucher.qf.ub.es) Grup de Cinetica i Dinamica de Reaccions Elementals DEPARTAMENT DE QUIMICA FISICA-UNIVERSITAT DE BARCELONA Marti i Franques, 1 08023 Barcelona SPAIN tel: ++34 93 402-1224 http://www.qf.ub.es/area3/jbm.html From chemistry-request@www.ccl.net Fri Sep 25 03:16:25 1998 Received: from foreman.ac.rwth-aachen.de (foreman.ac.RWTH-Aachen.DE [134.130.100.31]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA26565 Fri, 25 Sep 1998 03:15:29 -0400 (EDT) Received: (from landrum@localhost) by foreman.ac.rwth-aachen.de (AIX4.2/UCB 8.7/8.7) id JAA22350; Fri, 25 Sep 1998 09:12:43 +0200 (DFT) Date: Fri, 25 Sep 1998 09:12:37 +0200 (DFT) From: "Gregory A. Landrum" To: chemistry@www.ccl.net Subject: Form of Gaussian Basis Sets Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I have found myself in the vaguely uncomfortable position of wanting to make plots of orbitals from programs like Gaussian and GAMESS which use gaussian basis sets. I'm planning on adding this functionality to an existing plotting program, so I need the forms of the basis sets. So, this is probably a stupid question, but I'm completely fed up with trying to answer it myself... I can't seem to find the exact mathematical form of the basis sets used in these programs. The only things I can find are equations for the contracted radial basis functions. For example: \phi_i(r) = \sum_j [ d_{ij} exp(-f_j a_i r^2) ] (where I pull the {d} {f} and {a} values from the Gaussian output file or the basis set server at EMSL) I assume that I can combine this with the appropriate cartesian functions to get the correct *shape* of an orbital, but this doesn't do anything for me in terms of the *size* (because the resulting orbitals aren't normalized). So, my stupid question is: what is the exact mathematical form of these gaussian basis sets? Please don't point me at a book, because unfortunately our library is not likely to have it. Thanks in advance for your help. -greg -- --------------------- Dr. Greg Landrum (landrum@foreman.ac.rwth-aachen.de) Institute of Inorganic Chemistry Aachen University of Technology Prof.-Pirlet-Str. 1, D-52074 Aachen, Germany Phone: 049-241-80-7004 Fax: 049-241-8888-288 From chemistry-request@www.ccl.net Fri Sep 25 04:24:30 1998 Received: from csb0.IPC.PKU.EDU.CN (csb0.ipc.pku.edu.cn [162.105.177.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id EAA26686 Fri, 25 Sep 1998 04:24:02 -0400 (EDT) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA12297; Fri, 25 Sep 98 16:21:48 -0700 Date: Fri, 25 Sep 1998 16:21:47 -0700 (PDT) From: Fenglou Mao To: "CHEMISTRY@www.ccl.net" Subject: summary: free PC software Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I sent a mail about free PC software request of IR calculation and crystal building, but I got no response except some summary requests. I serarched it in Internet, I found a web site which may be useful. If you have time and same request as me, you can view it. These web site is: http://nhse.npac.syr.edu:8015/rib/repositories/csir/catalog/index.html You can found more links via this page. Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Peking University BeiJing P.R.China Tel:86-10-62751490 Fax:86-10-62751725 From chemistry-request@www.ccl.net Fri Sep 25 04:38:52 1998 Received: from dirac.cnrs-orleans.fr (dirac.cnrs-orleans.fr [163.9.6.67]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA26753 Fri, 25 Sep 1998 04:38:51 -0400 (EDT) Received: (from hinsen@localhost) by dirac.cnrs-orleans.fr (AIX4.3/UCB 8.8.8/8.7) id KAA20500; Fri, 25 Sep 1998 10:36:24 +0200 Date: Fri, 25 Sep 1998 10:36:24 +0200 Message-Id: <199809250836.KAA20500@dirac.cnrs-orleans.fr> X-Authentication-Warning: dirac.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: chemistry@www.ccl.net In-reply-to: <4195A3C6D39BD11189C30020AFFC17588F3BD9@vieexch1.vie.at.bic> (gerald.loeffler@vienna.at) Subject: Re: CCL:RE: CASP vs. The Tower of Babel References: <4195A3C6D39BD11189C30020AFFC17588F3BD9@vieexch1.vie.at.bic> > As a concrete example: It would be almost trivial to design an OO > framework for Energy Minimization (or Molecular Dynamics or Threading, > ...) where the force-field would be just one component that you "plug" > into the framework. The same is true for such algorithmic components as Of course; MMTK does it that way, and it works just fine. > But is the resulting code efficient? It's certainly a lot slower than > FORTRAN! (For language reasons and because you loose opportunities for > source-level optimizations if components have to be truly independent of > each other.) But I would argue that firstly speed of execution does not Loss of optimization is not a problem; if you consider what takes most of the time in computationally intensive algorithm, it's always energy evaluation, and that's always in one module (and a rather small one). The one point where I had to compromise for efficiency reasons is the interface between force field evaluation and the definition of the simulation universe. The latter defines how distances between atoms are calculated (e.g. minimum image convention), so the code should be in the universe module and not in the force field module. But distance calculations are used so frequently that the performance penalty of an indirect function per distance evaluation would be too high. I settled for a scheme that hard-codes the distance calculation into the force field routines for the common cases and uses an indirect function call for other (to be defined) univers shapes. Language/compiler issues are a different story. Since the numerics community has never shown much interest for anything but Fortran until recently, compiler manufacturers were under no pressure to work on code optimization for numerical problems in other languages. Some compilers do better than others; with a simple test case (hand-coded matrix multiplication) I found C/Fortran speed ratios between 1.1 and 100, depending on the machine. Moral: check compiler performance before buying a machine. However, you can still use Fortran for time-critical code (which is always a small part of a simulation program) and another language for the rest, at the price of worrying about machine-dependent interlanguage linking. I regularly use Fortran subroutines with MMTK, although the public distribution contains f2c-compiled code (less efficient) because I don't want to deal with questions about Fortran-C linking. In my opinion, the most important shortcoming in Fortran 9x is the lack of a standard interface with C. Such a standard interface would have made mixed-language programming the best solution for scientific software development (even if you don't like C, almost all languages have interfaces to C, so even Fortran-Pascal or Fortran-Lisp would be possible). > (Regarding unwillingness to give away source code at all: With Java you > can even give away the "object code" (byte code) (maybe after running it > through an obfuscator) and it will work on any Java platform...) True, but it's still like binary code; people can't inspect and modify it. And I would never use such programs for my scientific work, as far as calculations are concerned (I don't care about the source code for my text editor, of course). -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@www.ccl.net Fri Sep 25 06:12:01 1998 Received: from dndhost.ruc.dk (dndhost.ruc.dk [130.225.220.22]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA27057 Fri, 25 Sep 1998 06:11:59 -0400 (EDT) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by dndhost.ruc.dk (8.8.8+DND/8.8.8) with ESMTP id MAA18122; Fri, 25 Sep 1998 12:11:39 +0200 (MET DST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.40); 25 Sep 98 12:11:00 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.40); 25 Sep 98 12:10:47 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter Date: Fri, 25 Sep 1998 12:10:19 +0100 Subject: Re: CCL:Restraining dihedrals using HyperChem To: CHEMISTRY@www.ccl.net Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: Marcio Cyrillo, 21 Sep 1998: > - For molecular mechanics I understand this procedure of adding a > quadratic potential to the hamiltonian to restrain a variable, but it > seems to me as being meaningless to apply the same procedure to a > semi-empirical hamiltonian. Am I wrong? Empirical force fields may be added to a semiempirical Hamiltonian in order to correct for certain deficiencies. For example, J.J.P. Stewart added a torsional molecular-mechanics contribution to the semiempirical PM3 procedure in order to obtain the correct rotational barrier for C-N bonds in peptide linkages (MOPAC keyword MMOK). Another example is the attempt to correct for the poor performance of PM3 in the prediction of geometrical parameters for certain intramolecular hydrogen-bonds by the addition of a crude, empirical force field (actually constructed by using HyperChem's restraints option), see Spectrochim.Acta A53, 2615 (1997); Chem.Phys.Lett. 291, 51 (1998). > - In mopac we can easily accomplish the restraint of a variable - > changing a digit from 1 to 0 in the z-matrix scheme. Why did not > HyperChem use the same algorithm? With MOPAC it works fine, which is > pretty different in HyperChem where it almost impossible to, in fact, > restrain the variable to the desired value. Personally, I find HyperChem's restraints option a most useful feature, and I have had no problems restraining variables to the desired values. In a recent conformational study of phenyl- and (1-pyrenyl)triarylmethylcarbenium ions, torsional transition states were modelled by restraining selected dihedral angles (choosing HyperChem restraint 'force constant' k = 500), and even highly crowded transition states could be modelled in this way, see J.Org.Chem. 63, 1827 (1998). However, after the geometrical parameters have been optimized with inclusion of the restraints, a single point calculation WITHOUT RESTRAINTS should be run on the resulting structure in order to obtain the proper energy, otherwise small contributions from the restraint potentials may contaminate the predicted energy. Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://www.rub.ruc.dk/dis/chem/psos/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@www.ccl.net Fri Sep 25 08:41:38 1998 Received: from romeo.ic.ac.uk (romeo.ic.ac.uk [155.198.5.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id IAA27779 Fri, 25 Sep 1998 08:41:36 -0400 (EDT) Received: from oban.cc.ic.ac.uk [155.198.5.28] by romeo.ic.ac.uk with smtp (Exim 1.62 #1) id 0zMXBh-0003Vd-00; Fri, 25 Sep 1998 13:41:30 +0100 Received: from mtcmsag1.mt.ic.ac.uk ([155.198.96.22] helo=mtcmsa.mt.ic.ac.uk ident=root) by oban.cc.ic.ac.uk with smtp (Exim 1.90 #1) for CHEMISTRY@www.ccl.net id 0zMXBh-00014D-00; Fri, 25 Sep 1998 13:41:29 +0100 Received: from afmimage.mt.ic.ac.uk by mtcmsa.mt.ic.ac.uk (5.x/4.1) id AA06389; Fri, 25 Sep 1998 13:41:27 +0100 Message-Id: <3.0.5.32.19980925133004.00943b90@icex5.cc.ic.ac.uk> X-Sender: ic\seth\s.hogg@icex5.cc.ic.ac.uk X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32) Date: Fri, 25 Sep 1998 13:30:04 +0000 To: CHEMISTRY@www.ccl.net From: Simon Hogg Subject: xafs / exafs Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Is anyone aware of software to predict exafs / xafs spectra from crystal / molecular structure? Summaries as always ... -- Simon Hogg, Imperial College, London, UK Tel. +44 171 589 5111 ext. 56721 Fax. +44 171 584 3194 Email: s.hogg@ic.ac.uk Glass-List: glass-list@ic.ac.uk PGP: Key ID 0x4C048B49 Send "get public key" as subject for key FingerPrint B9C7 4E40 C73D 0E15 15E0 D6C6 79C4 AB59 4C04 8B49 From chemistry-request@www.ccl.net Fri Sep 25 09:25:30 1998 Received: from cliff.uottawa.ca (root@cliff.uottawa.ca [137.122.6.65]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA28015 Fri, 25 Sep 1998 09:25:29 -0400 (EDT) Received: from oreo.science.uottawa.ca (oreo.science.uottawa.ca [137.122.43.15]) by cliff.uottawa.ca (8.8.8/8.8.7) with ESMTP id JAA17716 for ; Fri, 25 Sep 1998 09:25:18 -0400 Received: from OREO/SpoolDir by oreo.science.uottawa.ca (Mercury 1.43); 25 Sep 98 09:25:43 GMT-5 Received: from SpoolDir by OREO (Mercury 1.43); 25 Sep 98 09:25:32 GMT-5 Received: from erik (137.122.43.165) by oreo.science.uottawa.ca (Mercury 1.43); 25 Sep 98 09:25:29 GMT-5 Sender: boufer@uottawa.ca Message-ID: <360B95AC.167E@cennas.nhmfl.gov> Date: Fri, 25 Sep 1998 09:07:56 -0400 From: boufer Organization: None X-Mailer: Mozilla 2.02 (X11; I; AIX 1) MIME-Version: 1.0 To: "Comp. Chem. List" Subject: Fitting a potential by a family of functions... Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Greetings all, I would like to ask you a question regarding potentials. I want to fit a potential~(of the Coulomb type) by some family of functions. My problem is, I cannot use the classical least square method in which we start by writing : D = Int (True Potential - approximation)^2 dv since in this case the true potential is not square integrable and hence yield to a divergence. Can any expert in this "business" suggest a reference describing the right procedure ? Thanks for your help. -- Ahmed From chemistry-request@www.ccl.net Fri Sep 25 11:25:32 1998 Received: from ifi.unicamp.br (lua.ifi.unicamp.br [143.106.6.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA28486 Fri, 25 Sep 1998 11:25:28 -0400 (EDT) Received: (from daemon@localhost) by ifi.unicamp.br (8.8.8/8.8.8) id MAA27398 for ; Fri, 25 Sep 1998 12:24:51 -0300 (BSC) From: Marcio Cyrillo - pos Received: from huckel.ifi.unicamp.br(143.106.72.134) via SMTP by lua.ifi.unicamp.br, id smtpdaaACca; Fri Sep 25 12:24:48 1998 Received: (from cyrillo@localhost) by huckel.ifi.unicamp.br (8.8.6/8.8.6) id MAA00341 for CHEMISTRY@www.ccl.net; Fri, 25 Sep 1998 12:24:46 -0300 (EST) Message-Id: <199809251524.MAA00341@huckel.ifi.unicamp.br> Subject: help! To: CHEMISTRY@www.ccl.net (Lista de Quimica) Date: Fri, 25 Sep 1998 12:24:46 -0300 (EST) X-Mailer: ELM [version 2.4 PL24] Content-Type: text Dear all, I wonder if someone can help me providing some information about at least one of the following two questions: 1 - Is it possible to access Matlab routines from a Visual Basic program? I know there is a .h file (C language) that incorporates the Matlab kernel, but I would like to have a .dll file with exportable functions to be used inside any other development enviroment. 2 - Having a collection of data of the following type: variable1, variable2, energy(variable1, variable2), is there a free (public) routine to plot the corresponding surface? I currently use Mathematica to plot these surfaces, but I would like not to depend on this commercial software. I hope someone can help me. These kind of information is important for me and may be important for other computational chemists as well. I would like to use this knowledge on a freeware I am developing. Thanks in advance, best regards, Cyrillo. From chemistry-request@www.ccl.net Fri Sep 25 12:07:52 1998 Received: from deimos.cber.nih.gov (deimos.cber.nih.gov [128.231.52.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA28658 Fri, 25 Sep 1998 12:07:52 -0400 (EDT) Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA237189411; Fri, 25 Sep 1998 12:03:31 -0400 Date: Fri, 25 Sep 1998 12:03:31 -0400 (EDT) From: Rick Venable To: chemistry@www.ccl.net Subject: Re: CCL:RE: CASP vs. The Tower of Babel In-Reply-To: <4195A3C6D39BD11189C30020AFFC17588F3BD9@vieexch1.vie.at.bic> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 23 Sep 1998, LOEFFLER,DR,GERALD FEM BENAT wrote: > So why is there no collaboration on the code-level between computational > scientists? There is; NETLIB is a good example, and there are a fair number of other ftp and web sites with excellent code available, covering a variety of scientific computational disciplines. The problem comes when you get to comprehensive packages in more specific application areas, such as those associated with computational chemistry. For that case, the answer is often money. For one thing, many of the better packages with academic roots have "gone commercial" in one way or another. Also, some academic groups use a modest charge for their source code as a means to fund the coding effort that supports their research. In some cases, universitities have chosen to "market" the products of their research groups, including research computer programs. In all of these cases, redistribution of source code is prohibited, although it may be available to non-profit researchers at little or no charge. An underlying issue is the ease-of-use factor; it still takes considerable effort to design and implement a rigorous and friendly graphical user interface, and someone needs to be paid to do that. Documentation is another factor, as is long term technical support (bugfixes, new features, etc.). -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov | \ / |=| position of the FDA; for that, http://www.erols.com/rvenable \/ |=| see http://www.fda.gov ) From chemistry-request@www.ccl.net Sat Sep 26 14:50:56 1998 Received: from tiger.jsums.edu (tiger.jsums.edu [143.132.85.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id OAA04992 Sat, 26 Sep 1998 14:50:55 -0400 (EDT) Received: by tiger.jsums.edu (951211.SGI.8.6.12.PATCH1502/930416.SGI.AUTO) for CHEMISTRY@www.ccl.net id NAA18163; Sat, 26 Sep 1998 13:54:55 -0500 Date: Sat, 26 Sep 1998 13:54:55 -0500 From: jerzy@tiger.jsums.edu (Jerzy Leszczynski) Message-Id: <199809261854.NAA18163@tiger.jsums.edu> To: CHEMISTRY@www.ccl.net Subject: CCTCC-7 Announcement Second Announcement Dear Colleague: We are pleased to announce the seventh conference on Current Trends in Computational Chemistry. This symposium, organized by Jackson State University, will cover all areas of computational chemistry as well as quantum chemistry. The local host of the conference is the US Army Corps of Engineers Waterways Experiment Station (WES) in Vicksburg, Mississippi. The meeting will be held at the Holiday Inn of Vicksburg, Mississippi (40 miles west of Jackson) on November 6 and 7, 1998. The format consists of a series of plenary lectures and poster presentations on Friday and Saturday, covering applications as well as theory. In addition, a banquet is scheduled for Friday evening and a dinner and reception for Saturday evening. The 7th conference will also feature another talk given in the ancillary "Noble Lecture Series." This series was initiated during the 6 CCTCC by a remarkable presentation by Istvan Hargittai entitled "The Molecules Among Us: Conversation with Famous Chemists." The lectures in this series are presented in a relaxed, after-dinner atmosphere by the noble speakers and are devoted to noble scientific events and people. As such, it is an exceptional lecture to the conference and contrary to the regular talks, might not necessarily report any Current findings. This year the talk will be delivered by Eiji Osawa who will speak on "Past and Future of the Fullerene Story." We are planning to publish extended abstracts (up to four pages each) of all invited talks and poster presentations. Original scientific contributions will be published in a special issue of the Journal of Molecular Structure (THEOCHEM). Manuscripts for inclusion in the special issue should be submitted in triplicate upon arrival at the registration desk. Submitted papers will be subject to the journal's standard referee procedures. Sincerely, Jerzy Leszczynski Chairman of the Organizing Committee INVITED SPEAKERS David Buckingham University of Cambridge "Molecules in Optical Fields" Stanley Burt NCI-Frederick Biomedical Supercomputer Center "The Use of DFT for Exploring Metal-Assisted Catalysis in Biology and Chemistry" Piet van Duijnen University of Groningen "Calculation of Electronic Properties of Molecules in Solution with Direct Reaction Field Method" William A. Goddard III California Institute of Technology TBA Magdolna Hargittai Hungarian Academy of Sciences "Metal Halide Molecular Structures: Interactions of Computations & Experiment" Ivan Hubac Comenius University, Bratislava "Non-adiabatic Molecular Hamiltonian. Canonical Transformations Coupling Electronic and Vibrational Motions" Kimihiko Hirao University of Tokyo "Recent Advances In Multireference Moller- Plesset Perturbation Theory" William L. Jorgensen Yale University "Computer Silmulations of Chemistry in Solution from Water to Protein-Ligand Binding" Modesto Orozco Universitat de Barselona "Theoretical Representation of Unsual DNA Structures" Eiji Osawa* Toyohashi University of Technology "Past and Future of the Fullerene Story" Pekka Pyykko University of Helsinki "Recent Results in the Theoretical Chemistry of Gold" Krishnan Raghavachari Bell Labs "Accurate Thermochemistry for Medium Sized & Large Molecles" David Singh Naval Research Lab "Toward Designer Materials Using First Principles Calculations" Krystyna Zakrzewska Institut de Biologie Physico-Chimique, Paris "Modelling Protein DNA Recognition" * After-dinner "Noble Lecture Series" 7TH CONFERENCE ON Current Trends In Computational Chemistry NOVEMBER 6 & 7, 1998, Vicksburg, Mississippi. 1. NAME:___________________________________________________________________ MAILING ADDRESS:________________________________________________________ ________________________________________________________________________ TELEPHONE: _____________ FAX: ______________ E-MAIL:__________________ 2. If you wish to present a poster, please indicate the title below. All abstracts are due by October 9, 1998 (up to 4 pages in length, presenting author underlined, photo ready quality, in duplicate) to ensure publication in the Conference Materials. TITLE:__________________________________________________________________ ________________________________________________________________________ AUTHORS:________________________________________________________________ 3. Conference materials, banquet and reception fee, all meals from breakfast Friday through dinner Saturday, coffee, and refreshments are included per paid participant. MAKE CHECKS PAYABLE TO: Current Trends in Computational Chemistry. Registration fee before September 1, 1998 US $150.00 $_________ Registration fee thereafter 200.00 $_________ Registration fee at student discount 75.00 $_________ 4. HOUSING: The organizers will not make housing reservations. To reserve a room at the special conference rate of $50.00-$60.00 per room, contact the Holiday Inn of Vicksburg, 3330 Clay Street, Vicksburg, MS 39180, Tel:(601)636-4551, Fax:(601)636-4552. Reservations should be arranged with the Holiday Inn prior to October 10, 1998. I do _____ do not _____ plan to stay at the conference hotel. I do _____ do not _____ plan to submit a paper to the special issue of THEOCHEM. ____________________ Signature http://tiger.jsums.edu/~cctcc Department of Chemistry, Jackson State University, Jackson, MS 39217, USA Conference Chairman: Dr. Jerzy Leszczynski, Tel: 601-973-3482, Email: jerzy2.iris5.jsums.edu. Conference Secretary: Ms. Shonda Allen, Tel: 601-973-3723, Email: srallen@stallion.jsums.edu.