From schlecmf@esvax.dnet.dupont.com Thu Dec 7 15:38:24 1995 Received: from gatekeeper.es.dupont.com for schlecmf@esvax.dnet.dupont.com by www.ccl.net (8.6.10/950822.1) id PAA21526; Thu, 7 Dec 1995 15:38:17 -0500 From: Received: by gatekeeper.es.dupont.com; id AA27614; Thu, 7 Dec 95 15:38:11 -0500 Received: by esds01.es.dupont.com; id AA16252; Thu, 7 Dec 95 15:38:03 -0500 Message-Id: <9512072038.AA16252@esds01.es.dupont.com> Received: from esvax.dnet; by esds01.dnet; Thu, 7 Dec 95 15:38:10 EST Date: Thu, 7 Dec 95 15:38:10 EST To: chemistry@www.ccl.net Subject: Units Conversion Regarding the recent inquiry on units conversion, > Could anyone come up with reasonable accuracy (at least 6 significant > figures) for > > Hartrees to Joules > Calories to Joules > Bohr to Angstrom > > Non of my texts even have the definition of a Hartree. > > Thanks in advance > > Alex > > +--------------------------------------------------+ > |Alternate E-mail A.J.Turner@Bath.ac.uk | > |www home @ http://www.bath.ac.uk/~chpajt/home.html| > +--------------------------------------------------+ I can recommend a WWWeb site which will carry out such conversions interactively: http://www.chemie.fu-berlin.de/chemistry/general/units.html Instructions are given in English and German, but it is simple to use. Submitting the requested conversion queries to this resource gave the following answers. 1 hartree = 4.359748e-18 joule 1 calorie = 4.1868 joule (fewer than the requested six significant figures) 1 bohrradius = 0.5291772 angstrom This server is often busy, so reference to a manual will often provide the answer quicker. From sz1296@rzmail.uni-erlangen.de Thu Dec 7 08:00:04 1995 Received: from max3.rrze.uni-erlangen.de for sz1296@rzmail.uni-erlangen.de by www.ccl.net (8.6.10/950822.1) id HAA09238; Thu, 7 Dec 1995 07:59:49 -0500 From: Received: from cd4680fs.rrze.uni-erlangen.de by max3.rrze.uni-erlangen.de; Thu, 7 Dec 95 12:43:55 +0100 Received: from local by cd4680fs (5.61/cl-RRZE) id AA26751; Thu, 7 Dec 95 12:43:54 +0100 Subject: help To: chemistry@www.ccl.net Date: Thu, 7 Dec 95 12:43:53 MET Message-Id: <30c6d37b30cb002@max3.rrze.uni-erlangen.de> Dear CCL users, A friend of mine who hasn't got a proper access to internet is seeking information about [W(CO)3(Cp)Cl] (Cp= Cyclopentadienyl). (I hope I got that right) He'd like to know something about the use of that substance, spectroscopic data or anything else. As I am NOT subscribed to the CCL, please send a copy of your answer to me, that is: sz1296@rrze.uni-erlangen.de Thank you very much in advance From states@ibc.WUStL.EDU Thu Dec 7 17:43:56 1995 Received: from medicine.wustl.edu for states@ibc.WUStL.EDU by www.ccl.net (8.6.10/950822.1) id RAA24234; Thu, 7 Dec 1995 17:43:53 -0500 Received: from ibc.WUStL.EDU (bison [128.252.122.174]) by medicine.wustl.edu (8.7/8.7) with SMTP id QAA06549 for ; Thu, 7 Dec 1995 16:41:20 -0600 (CST) Received: from ibc (localhost) by ibc.WUStL.EDU (5.x/SMI-SVR4) id AA17041; Thu, 7 Dec 1995 16:43:52 -0600 Sender: states@ibc.wustl.edu Message-Id: <30C76E28.30B@ibc.wustl.edu> Date: Thu, 07 Dec 1995 16:43:52 -0600 From: "David J. States" Organization: Institute for Biomedical Computing Mime-Version: 1.0 To: chemistry@www.ccl.net Cc: states@ibc.wustl.edu Subject: Call for Papers - Intelligent Systems for Molecular Biology '96 The Fourth International Conference on Computational Biology Intelligent Systems for Molecular Biology '96 June 12-15, 1996 Washington University, St. Louis, Missouri, USA http://ibc.wustl.edu/ismb96 Call For Papers An electronic mailing list can be joined by sending a message to ismb96@ibc.wustl.edu with the word "subscribe" as the body of the message. Key Dates Meeting: June 12-15, 1996 Paper Submissions Papers due: Feb 1, 1996 Replies to authors: Mar 15, 1996 Revised papers due: Apr 1, 1996 Open Poster Submissions Abstracts due: Apr 1, 1996 Tutorial Proposals Full proposals due: March 18, 1996 Replies to authors: April 1, 1996 Draft handouts due: April 15, 1996 Final handouts due: May 13, 1996 Tutorials presented: June 12, 1996 The purpose of the ISMB conference is to disseminate the latest developments in computational molecular biology and biophysics and to stimulate new work on the application of intelligent computational systems to problems in molecular biology. ISMB is a multidisciplinary conference bringing together scientists from computer science, mathematics, statistics, and molecular biology. Its scope extends to any computational method or system supporting a biological task that is algorithmically, cognitively, or conceptually challenging, involves a synthesis of heterogeneous information, or exhibits the emergent properties of an "intelligent system." From a computational perspective, areas of interest include adaptive systems, intelligent experimental control, data modeling, machine learning, artificial intelligence, combinatorics, stochastic optimization, string and graph algorithms, linguistic methods, and parallel computer technologies. Biological areas of interest include molecular structure, genomics, molecular sequence analysis, evolution and phylogenetics, adaptive experimental systems, and molecular biology. Emphasis is placed on the validation of methods using real data sets and on practical application in the biological sciences. The ISMB conference has attracted a large and enthusiastic audience comprising scientists involved in application areas such as artificial intelligence, structural biology, DNA, RNA and protein sequence analysis and structure prediction, genome mapping, gene identification, molecular biology data and knowledge bases, and the modeling of biochemical processes. We are continuing the tradition of soliciting original papers, which will be rigorously refereed and published (by AAAI Press and the MIT Press) in proceedings available at the conference. The conference proceedings are indexed in the Medline database. The previous ISMB meetings were 1993: National Library of Medicine, USA 1994: Stanford University, USA 1995: Cambridge University, UK The four-day conference will feature introductory and advanced tutorials on June 12th and presentations of original refereed papers, posters, and invited talks (June 13-15). There will be special sessions at the conference on "Whole Genomes: Challenges and Implications," and on the "Interconnection of Molecular Biology Databases (MIMBD)." A test suite of raw data will be set aside to evaluate base-calling and gene-finding programs. A job fair and a vendor fair are also being organized. Organizing committee David States (states@ibc.wustl.edu) Terry Gaasterland (gaasterl@mcs.anl.gov) Randall Smith (rsmith@imgen.bcm.tmc.edu) Keynote Speakers Robert Waterston, Washington Univ., St. Louis David Haussler, Univ. of California, Santa Cruz Russell Doolittle, Univ. of California, San Diego Chris Sander, EMBL, Heidelberg Contact address ISMB '96 Institute for Biomedical Computing Washington University School of Medicine 700 South Euclid Avenue St. Louis, MO 63110-1012 USA Phone: (314) 362-2134 FAX: (314) 362-0234 From hoaren@cv.port.ac.uk Thu Dec 7 12:07:45 1995 Date: Thu, 07 Dec 1995 17:04:40 EST To: chemistry-request@ccl.net Message-ID: <0099A84E.8F6E0D00.72@cv.port.ac.uk> From: "Dave THURSTON (Pharmacy)" Organization: University of Portsmouth To: chemistry-request@ccl.net Date: Wed, 6 Dec 1995 07:43:02 GMT Subject: Drug.dna ListServer (New) Dear Colleague, I am writing to ask you whether you would be interested in joining an E-Mail ListServer dedicated to those of us interested in the area of Drug-DNA interactions. To the best of my knowledge there is no ListServer currently available that is dedicated to this cause, although snippets of information turn up on a number of international Medicinal Chemistry and Organic Chemistry Bulletin Boards and ListServers. I thought, therefore, that the time is right to set one up. For those of you not too familiar with ListServers, the idea is that you subscribe to the "List" by sending a simple E-Mail message. Once subscribed, if you have something interesting to say about Drug-DNA interactions - perhaps a paper that has recently interested you, a point made at a recent conference, or a question that someone else may be able to help with - you simply send the message to the List. The computer programme then automatically sends your comment/question out to everyone on the List. When a ListServer works well, it is almost equivalent to a "Virtual Conference". Working well depends on the enthusiasm and support of those subscribed - so I do hope you will join me in this venture. To subscribe to the List, please send an E-Mail message to: maiser@sci.port.ac.uk There is no need to give a Subject Title to your message. However, on the first line of the body of the text to your message, please write: subscribe drug.dna Please put a "Return" at the end of this line to avoid any headers being added automatically by your own software. You should then receive a message from the ListServer with information about your subscription. You will then be ready to start communicating with other List members. Obviously it may take a few weeks (or even months) for the number of subscribed members to reach the level where useful exchanges of information can take place. However, it is worth being patient. Once I have detected a "core" number of subscribed members, say 50 to 100, I will ask everyone to send a brief message to introduce themselves to other List members. Please pass this E-Mail message on to any colleagues (either in the UK or elsewhere) who may be interested in drug-DNA interactions. Perhaps you would also pass it on to any chemically-oriented ListServers or Bulletin Boards to which you belong. Hope to see you on the List. With Kind Regards David E. Thurston Professor David E. Thurston Anti-Cancer Drug Design Unit Division of Medicinal Chemistry School of Pharmacy University of Portsmouth Park Building King Henry Ist Street Portsmouth, Hants. PO1 2DZ UK Internet: Thurstonde@phar.port.ac.uk Phone: +44 01705-842632 (Direct/Answer Phone) Mobile: 0973-499429 (Orange Network) Fax: +44 01705-84262 From M.Langoor@ams.chem.ruu.nl Thu Dec 7 05:36:15 1995 Received: from ams.chem.ruu.nl for M.Langoor@ams.chem.ruu.nl by www.ccl.net (8.6.10/950822.1) id FAA07377; Thu, 7 Dec 1995 05:36:13 -0500 Received: from [131.211.60.238] by ams.chem.ruu.nl with SMTP (Apple Internet Mail Server 1.0); Thu, 7 Dec 1995 11:35:59 +0100 X-Sender: M.Langoor@ams.chem.ruu.nl (Unverified) Message-Id: To: chemistry@www.ccl.net From: M.Langoor@ams.chem.ruu.nl (Marcel Langoor) Subject: CCL:H-bond accuracies within MM3 Date: Thu, 7 Dec 1995 11:35:59 +0100 Dear netters, I'm using MM3(92) to calculate conformations of compounds with intramolecular hydrogen bonds. From the resulting (energy-minimized) structures I obtain parameters like e.g. d(H...X) and <(X-H...X), i.e. the distance between donor- and acceptor-atom and the often used "hydrogen bond angle", respectively. My question is: What are the accuracies in the above mentioned parameters ? (Are we talking about 0.01 or 0.1 Angstrom ? and 1 or 10 degrees ?) Please respond if somebody has any ideas about this topic or perhaps literature references on it. If there is enough interest I will send a summary to the net. Thanking you in advance. Marcel --------------------------------------------------- Marcel H. Langoor Utrecht University Dept. of Analytical Molecular Spectrometry Section IR/Raman P.O. Box 80083 3508 TB Utrecht phone +31 30 2536811 fax +31 30 2518219 e-mail: m.langoor@ams.chem.ruu.nl --------------------------------------------------- From moshe_o@VNET.IBM.COM Tue Dec 5 07:02:45 1995 Received: from VNET.IBM.COM for moshe_o@VNET.IBM.COM by www.ccl.net (8.6.10/950822.1) id HAA00118; Tue, 5 Dec 1995 07:02:42 -0500 Message-Id: <199512051202.HAA00118@www.ccl.net> Received: from HAIFASC3 by VNET.IBM.COM (IBM VM SMTP V2R3) with BSMTP id 8819; Tue, 05 Dec 95 07:02:29 EST Date: Tue, 5 Dec 95 14:02:34 IST From: "Moshe Olshansky" To: chemistry@www.ccl.net Subject: combining basis sets - an addition Dear netters! About a week ago I asked the following question: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ P.S. and now I have an additional question: I am a mathematician, not a chemist, so let me look at the basis sets purely mathematically. If one has a complete (and hence necessarily infinite) basis set, he/she gets a limit of Hartree-Fock model. Otherwise (with limited basis set) one gets some approximation to this limit and the more complete the basis set is the better is the approximation. Now assume one uses a certain "standard" basis set and gets some result (from Hartree-Fock model). And now we add ANY additional function to this basis set. This does not make the basis set less complete and so it should lead to at least as good (or even better) an approximation as the original basis did (it is also possible to get the original solution by taking that additional function with zero coefficient for every electron). Is there anything wrong with this statement? ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ I want to thank all those who replied. As I understand, adding just any function will indeed lower the model energy but the problem is that for unbalanced basis set the wave function with lower energy does necessarily better describe the chemical properties. Below are the responses I received. Moshe Olshansky e-mail: moshe_o@vnet.ibm.com ========================================================================= Date: Tue, 28 Nov 95 10:08:10 -0600 From: smb@smb.chem.niu.edu (Steven Bachrach) Yes, the addition of an extra function MUST result is an energy equal or lower than obtained with the smaller basis set. Having a balanced basis set is only important in two circumstances (1) when you are far from the HF limit (i.e. using a small basis set) and need to get as much of the "correct"soultion as possible (2) when you are trying to do some type of density decomposition in terms of orbital occupancy. Realize that one could describe the LiF molecule with simply a huge number of basis functions centered on just Li. The solution would be identical to one obtained with a large number of orbitals centered on both atoms. Steve Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 ========================================================================= Date: Tue, 28 Nov 1995 13:08:57 -0330 (NST) From: Uli Salzner Subject: basis stes Dear Moshe, it is correct that by adding any function to a basis set you get a mathematically improved representation of the wavefunction. The total energy will be lower. The danger is that you might introduce physical or chemical errors by lowering the energy unevenly for the different atoms. The electrons will then flow to the regions where their energy is lower. Try to calculate ethane with an STO-3G basis set on one carbon atom and 6-311+G* on the other carbon and check the charges of both carbons. Mathematically the wavefunction is certainly more complete than with STO-3G on both carbons but the calculation will not reproduce the chemical fact that both carbons are identical. In a geometry optimization not only the distribution of the electrons but also the position of the atoms can be influenced by an unbalance basis set. The reason is that if you use a small basis set, the energy of the molecule gets lower when the atoms are closer together and can use the functions of the neighbor, thus improving their basis sets. This can be due to insufficient basis sets on all atoms or on only one. If you want to see the effect of using different basis sets on a chemical problem, you may look at the results we got for the bond angle of CaF2 with different basis sets: U. Salzner and P. v. R. Schleyer, Chem. Phys. Lett. 1990, 172, p461. Fortunately the problem is normally less severe. CaF2 is an extrem case because the potential energy surface is v e r y flat. Bye, Uli ========================================================================= From: gunnj@CERCA.UMontreal.CA Date: Tue, 28 Nov 1995 12:08:52 -0500 (EST) It depends what you mean by 'better'. What you describe will lower the energy, since that is the function you are variationally minimizing. There is no guarantee that any other function, like the dipole moment for example, will converge 'smoothly' as you add basis functions. Furthermore, the HF approximation is not necessarily very accurate, so approaching that limit might not be what you intuitively expect as an improvement. -- John Gunn (gunnj@cerca.umontreal.ca) | "The world will not be free until Departement de Chimie / CERCA | the last king is strangled with Universite de Montreal | the entrails of the last priest." ========================================================================= Date: Tue, 28 Nov 1995 12:20:15 -0500 From: ryszard@msi.com (Ryszard Czerminski X 217) Dear Moshe, I am not chemist either (I am physicist) so let me say what is my understanding of the concept of "balanced basis set". Your statement that adding "ANY additional function" will make results at least as good is definitely true in the sense that it will produce at least as low total energy as wave function without it. On the other hand this is not always the value you are after. Sometimes you are interested in charge distribution (dipole moments etc...), sometimes in energy differences (when studying molecular complexes). In such cases adding any arbitrary function might make your results worse not better, because these values are not covered by variational principle. This is why, to some extend, generating "well balanced basis set" is sort of "alchemical art" to me. As I understand it, this is the question of compromise between resources (CPU time, memory, etc....) and quality of results for values not necessarily obtained from variational principle (in usual formulation it covers only expected value of the hamiltonian i.e. total energy of the system). With unlimited computational resources the whole idea of well balanced basis sets would be moot. Best regards, Ryszard Czerminski +--------------------------------------------------------------+ | Biosym/Molecular Simulations | phone : (617)229-8875 x 217 | | 16 New England Executive Park, | fax : (617)229-9899 | | Burlington, MA 01803-5297 | e-mail: ryszard@msi.com | +--------------------------------------------------------------+ ========================================================================= Date: Tue, 28 Nov 1995 14:03:26 -0500 (EST) From: "E. Lewars" Hello, This is a comment on your query as to whether increasing the size of a basis set should always improve the calculated results. In practice it does not always give better results (see Warren Hehre, "Practical Methods for Electronic Structure Calculations", Wavefunction Inc., 1995). As a mathematician, you realize we are trying to span an infinite-dimentional vector space with a finite basis set, and it seems that as this set gets bigger the results should get better. However, there is no guarantee that the approach to perfection is smoothly asymptotic; it may oscillate. And in fact a bigger basis set *can* lead to worse results. Best Wishes Errol E. Lewars ========================================================================= Date: Tue, 28 Nov 1995 11:49:18 -0800 From: Rene Fournier Hello ; What you wrote is correct in a sense, but one has to be careful about what is meant by "good" or "better". By virtue of the "variational principle", adding ANY basis function will lower the total Hartree-Fock energy (the energy required to pull to infinity all electrons while keeping the nuclei fixed) and it will get closer to the true total energy. In that sense, results are better. However we are always interested in energy DIFFERENCES, NOT the total energy. Say you underestimate the bond energy of a diatomic AB with a certain basis set and when you add certain functions the energies of A, B, and AB all go down, by 0.1 eV, 0.2 eV, and 0.25 eV respectively. You have better total energies for each of A, B and AB but the dissociation energy is smaller by 0.05 eV and worst than the original one. I think this situation is common with small or medium size basis sets, and not only for dissociation energies but for all properties related to energy differences: ionization potentials, electron affinities, excitation energies, barriers to reaction, harmonic vibrational frequencies, energy differences between conformers, equilibrium geometries. If one judges the quality of results with respect to experiment the issue becomes even more cloudy. If a limit Hartree-Fock calculation overestimates a bond length by 0.10 Angstrom, then using a certain grossly incomplete basis set might bring the Hartree-Fock calculation in perfect agreement with experiment but in error by 0.10 Angstrom from the complete basis set result. Is that good or bad ? It is good in the context of an empirical approach that works systematically, but it is bad if one has an "ab initio" approach. For example, scaled harmonic frequencies calculated by Hartree-Fock with some small basis are "good" from an empirical point of view. My overall impression from the quantum chemistry literature is this. When using a small or medium basis set, adding basis functions can worsen energy differences almost as likely as they can improve it, unless one uses "chemical intuition" to choose precisely what basis functions to add. When using very large basis sets, I think that adding more basis functions almost always improves all results (or leaves them unchanged). Here is a humoristic illustration of this. This graph pretends to show the error on a typical property measured relative to experiment as a function of the level of theory and the "3 zero-error regions" where quantum chemists try to work: "Pauling's", "HF/6-31G" (or today we might say "BLYP//6-31G" ?!), and the "really good calculation". A similar graph may apply also if the x-axis was labeled "basis set size" and the graph referred only to Hartree-Fock calculations with error measured relative to limit Hartree-Fock. ( Note: I made this graph from memory from a similar one I saw in a lecture by P. O. Lowdin; my apologies for possible inacurracies or misrepresentation. I think it was a very good graph! ) ^ | | | x x E |x r |x r |x o |x r | x | x | x | x Really, REALLY tough | x x x / fully ab initio | x Pauling's level x x / calculation | x of theory x x / | x / x x | x / x |---> x | x / x |---> x 0| |x | | x | | x ----|---|-x-|-------|--x--|------------------|-----------------------x---> |0 | x | | x | | Level of theory; | x x \ Computational effort | x x \ | x x \ | x x Hartree-Fock 6-31G | level of theory Sincerely, Rene Fournier. |-------------------------------|-----------------------------| | Rene Fournier | fournier@physics.unlv.edu | | Department of Physics | fournie@ned1.sims.nrc.ca | | University of Nevada | phone : (702) 895 1706 | | Las Vegas, NV 89154-4002 USA | FAX : (702) 895 0804 | |-------------------------------|-----------------------------| ========================================================================= Georg Schreckenbach Tel: (Canada)-403-220 8204 Department of Chemistry FAX: (Canada)-403-289 9488 University of Calgary Email: schrecke@zinc.chem.ucalgary.ca 2500 University Drive N.W., Calgary, Alberta, Canada, T2N 1N4 ============================================================================== From: "Victor M. Rosas Garcia" Date: Tue, 28 Nov 1995 23:02:46 -0500 I'm a chemist, not a mathematician, but I like this kind of problems so, here I go: I'd say, yes, there is something wrong with the statement. First I want to point out what I consider is a small contradiction in your argument, first you say: "let me look at the basis sets purely mathematically" which I understand as dismissing any considerations of "physical meaning". Then you say: "If one has a complete (and hence necessarily infinite) basis set, he/she gets a limit of Hartree-Fock model." Now we are considering the basis sets within the frame of a physical model (the Hartree-Fock approximation) and therefore we are not considering them purely mathematically. Having said that, my reasoning is as follows: Inasmuch as the basis set complies to certain requirements of the physical model (e.g. a functional form that will "imitate" Slater Type Orbitals), the addition of ANY function (which in the general case does not comply to those requirements) will affect negatively the result of the calculation. I mean, as far as the Hartree-Fock model is concerned. just my $0.02 Victor -- ----------------------------------------------------------------------- Victor M. Rosas Garcia * "How can we contrive to be rosas@irisdav.chem.vt.edu * at once astonished at the Virginia Tech doesn't necessarily share * world and yet at home in it?" the opinions you just read. * G. K. Chesterton ------------------------------------------------------------------------- ========================================================================= Date: Wed, 29 Nov 1995 11:10:00 +0100 From: peon@medchem.dfh.dk (Per-Ola Norrby) It of course depends on what you mean with "better". The SCF will minimize the energy, adding any new function should give an energy closer to the HF limit. However, most of the time this is not really interesting. When you want energies, you usually want relative energies, and then it's quite important that you make the same approximations, that is, calculate at a constant level of theory, so that systematic errors cancel. Also, as you said in the part of the message I deleted, adding functions in an unbalanced way will definitely affect the charge distribution, probably not making it "better" :-) Specific questions can sometimes be answered by including functions that are not atom-centered, but then you get the problem of findning a completely reproducable way of doing that for any system. Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ --- Bureaucracy is a challenge to be conquered with a righteous attitude, a tolerance for stupidity, and a bulldozer when necessary -- Peter's Law 15. * Per-Ola Norrby * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, peo@compchem.dfh.dk ========================================================================= Date: Wed, 29 Nov 1995 13:25:18 +0100 (NFT) From: oppel@pctc.chemie.uni-erlangen.de Dear Moshe, concerning your question about adding any basis-function to an existing basis-set, I think you are right in principle, that this function doesn't make the basis worse, i.e., the energie becomes 'better' in the sense, that it reaches the exact solution. BUT, often the energy is not the quantity a chemist is interested in. Especially, if one takes a look at the charges at a certain atom in a system, one uses the so-called Mulliken-analysis (as you may know), to get this information. Unfortunatly, this quantity isn't even an obsevable, so one cannot get it be taking the expectation-value of an hermitian operator. One takes the difference between the nuclear charge at the atom and the sum of the diagonal-elements of P*S, which belong to this atom. Now, if you have an unbalanced basis-set, you will get charges which are far from reality. In the worst case, think of a complete basis, where all the functions are centered on a single atom. If you do now a Mulliken-analysis, you will find no electrons on the other atoms, though the solution of the HF-equations is exact. So, take care of your basis-set, and choose it well for the chemical problem you have to solve. Markus Oppel Chair for theoretical chemistry University of Erlangen-Nuernberg Germany oppel@pctc.chemie.uni-erlangen.de From S.R.Kilvington@soton.ac.uk Fri Dec 8 11:48:35 1995 Received: from beech.soton.ac.uk for S.R.Kilvington@soton.ac.uk by www.ccl.net (8.6.10/950822.1) id LAA07309; Fri, 8 Dec 1995 11:48:32 -0500 Received: from willow.soton.ac.uk (willow.soton.ac.uk [152.78.128.20]) by beech.soton.ac.uk (8.6.12/hub-8.5a) with ESMTP id QAA03425 for ; Fri, 8 Dec 1995 16:46:22 GMT Received: (from srk@localhost) by willow.soton.ac.uk (8.6.10/client-8.8) id QAA05533 for CHEMISTRY@www.ccl.net; Fri, 8 Dec 1995 16:42:34 GMT Message-Id: <199512081642.QAA05533@willow.soton.ac.uk> Subject: Re: Problem in reading PDB files To: CHEMISTRY@www.ccl.net Date: Fri, 8 Dec 1995 16:42:34 +0000 (GMT) From: "Simon Kilvington" > > Have you ever used SYBYL? During the last few days, I was astonished to > find SYBYL does have problem in reading PDB files. Let me elaborate now. > [troubles with aromatic atoms deleted] the problem is PDB files don't have any data explicitly stored in them about bond orders and atom hybridisations. As the PDB format was initially designed to store protein structures it was assumed that all the molecules would be composed of only atoms in the twenty common amino acids. Therefore the residue field ie (TRP, PRO, etc) is used to look up a template which describes the connectivity [and bond type?]. now people are using PDB as a general molecule format and this causes problems. there should be no reason to use PDB files for storing general molecular structures because there are already *far* too many chemical structure file formats and most of these allow you to store connectivity, bond order, and hybridisation information. if I were you I would use a file format like MOL2 - this is text based, free format, and capable of storing a wide variety of information. even if you need to import your structure files into a program that doesn't support MOL2 files you can use the invaluable program BABEL to convert it. I think a standard molecule file format is needed. What happened to the chemical MIME type? is this still being designed or is it all agreed on yet? -- Simon Kilvington, srk@soton.ac.uk From hinsenk@ERE.UMontreal.CA Sun Dec 10 09:27:31 1995 Received: from harfang.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.10/950822.1) id JAA07780; Sun, 10 Dec 1995 09:27:07 -0500 Received: from eole.ERE.UMontreal.CA (eole.ERE.UMontreal.CA [132.204.10.20]) by harfang.CC.UMontreal.CA with ESMTP id JAA12148 (8.6.11/IDA-1.6); Sun, 10 Dec 1995 09:25:19 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (950221.405.SGI.8.6.10/5.17) id JAA12847; Sun, 10 Dec 1995 09:25:18 -0500 Received: by cyclone.ERE.UMontreal.CA (950221.405.SGI.8.6.10/5.17) id JAA04554; Sun, 10 Dec 1995 09:25:18 -0500 Date: Sun, 10 Dec 1995 09:25:18 -0500 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <199512101425.JAA04554@cyclone.ERE.UMontreal.CA> To: schlecmf@esvax.dnet.dupont.com CC: chemistry@www.ccl.net In-reply-to: <9512072038.AA16252@esds01.es.dupont.com> (schlecmf@esvax.dnet.dupont.com) Subject: Re: CCL:Units Conversion I can recommend a WWWeb site which will carry out such conversions interactively: ... My recommendation for people who have to deal with unit conversions often is to get a copy of GNU-Calc, a free calculator add-on for the GNU-Emacs editor. Among other useful features (ranging from matrix computations to graphics, and including even elemetary symbolic calculations) it has a very flexible unit conversion system that lets you even complicated units easily. It can be found wherever you can get GNU software. 1 calorie = 4.1868 joule (fewer than the requested six significant figures) Because 4.1868 J is exact - by definition. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. Centre-Ville | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From Darren.Andrews@man.ac.uk Sun Dec 10 10:57:33 1995 Received: from nessie.mcc.ac.uk for Darren.Andrews@man.ac.uk by www.ccl.net (8.6.10/950822.1) id KAA08554; Sun, 10 Dec 1995 10:46:58 -0500 Received: from [130.88.12.235] (actually femt03.ch.man.ac.uk) by nessie.mcc.ac.uk with SMTP (PP); Sun, 10 Dec 1995 15:46:35 +0000 X-Sender: mbcdpa@nessie.mcc.ac.uk Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Sun, 10 Dec 1995 15:47:19 +0000 To: chemistry@www.ccl.net From: Darren.Andrews@man.ac.uk (Darren Andrews) Subject: AM1 Parameters for Magnesium Can anyone provide good Semi-Empirical parameters for Magnesium, preferrably for AM1 calculations. Darren.Andrews@man.ac.uk From elewars@alchemy.chem.utoronto.ca Sun Dec 10 14:42:36 1995 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.10/950822.1) id OAA10622; Sun, 10 Dec 1995 14:41:01 -0500 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.1/8.7.1) id OAA24619 for chemistry@www.ccl.net; Sun, 10 Dec 1995 14:40:58 -0500 (EST) Date: Sun, 10 Dec 1995 14:40:58 -0500 (EST) From: "E. Lewars" Message-Id: <199512101940.OAA24619@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: MATRIX ALGEBRA PROGRAM Hello, Could someone suggest a free program for the PC that will do matrix diagonalization and matrix multiplication? Thanks. Errol Lewars ==== From JUNG@Jetson.UH.EDU Sun Dec 10 14:48:13 1995 Received: from Sumtoi.UH.EDU for JUNG@Jetson.UH.EDU by www.ccl.net (8.6.10/950822.1) id OAA10535; Sun, 10 Dec 1995 14:30:09 -0500 From: Received: from Jetson.UH.EDU by Jetson.UH.EDU (PMDF V4.3-10 #8380) id <01HYN6QGDD9S8Y5X0W@Jetson.UH.EDU>; Sun, 10 Dec 1995 13:30:08 -0600 (CST) Date: Sun, 10 Dec 1995 13:30:08 -0600 (CST) Subject: AM1 parameters for Silicon. To: chemistry@www.ccl.net Message-id: <01HYN6QGEFUQ8Y5X0W@Jetson.UH.EDU> X-Envelope-to: chemistry@www.ccl.net X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netter I need to calculate sp3-slilcon in cyclic system suc 1,5-cyclooctadiene or 1,3,5-cyclooctatrien like systems. Can anyone have good Semi-Empirical parameters for silicon preferrably for AM1. Any kind information how to handle these kind of system, I would be appreciated. Thank you Jung@jetson.uh.edu From JUNG@Jetson.UH.EDU Sun Dec 10 14:57:36 1995 Received: from Sumtoi.UH.EDU for JUNG@Jetson.UH.EDU by www.ccl.net (8.6.10/950822.1) id OAA10656; Sun, 10 Dec 1995 14:43:54 -0500 From: Received: from Jetson.UH.EDU by Jetson.UH.EDU (PMDF V4.3-10 #8380) id <01HYN7F8E1EU8Y5X0W@Jetson.UH.EDU>; Sun, 10 Dec 1995 13:43:12 -0600 (CST) Date: Sun, 10 Dec 1995 13:43:12 -0600 (CST) Subject: AM1 patameters for AM1 To: chemistry@www.ccl.net Message-id: <01HYN7F8E1EW8Y5X0W@Jetson.UH.EDU> X-Envelope-to: chemistry@www.ccl.net X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netter I need to calculate sp3-slilcon in cyclic system suc 1,5-cyclooctadiene or 1,3,5-cyclooctatrien like systems. Can anyone have good Semi-Empirical parameters for silicon preferrably for AM1. Any kind information how to handle these kind of system, I would be appreciated. Si-Si Si-Si / \ / \ C C C C || || || || C C C C \ / \ / C = C Si-Si Thank you Jung@jetson.uh.edu From sscu.iisc.ernet.in!ananth@vigyan.iisc.ernet.in Sun Dec 10 15:57:37 1995 Received: from relay7.UU.NET for sscu.iisc.ernet.in!ananth@vigyan.iisc.ernet.in by www.ccl.net (8.6.10/950822.1) id PAA11214; Sun, 10 Dec 1995 15:45:39 -0500 Received: from iisc.ernet.in by relay7.UU.NET with SMTP id QQztod03934; Sun, 10 Dec 1995 15:45:28 -0500 (EST) Received: from vigyan.UUCP by iisc.ernet.in (ERNET-IISc/SMI-4.1) id AA06605; Mon, 11 Dec 95 02:20:47+0530 Received: by vigyan.iisc.ernet.in (smail2.3) id AA26596; 11 Dec 95 02:11:56 EST (Mon) Received: by sscu (Smail3.1.28.1 #4) id m0tOtbl-000E4AC; Sun, 10 Dec 95 13:48 PST Date: Sun, 10 Dec 1995 13:48:30 +0000 From: "S.P.Ananthavel" Subject: Re: CCL:MATRIX ALGEBRA PROGRAM To: "E. Lewars" Cc: chemistry@www.ccl.net In-Reply-To: <199512101940.OAA24619@alchemy.chem.utoronto.ca> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hallo, you can try with MATLAB . if you have any problem write to me ananth On Sun, 10 Dec 1995, E. Lewars wrote: > Hello, Could someone suggest a free program for the PC that will do > matrix diagonalization and matrix multiplication? > Thanks. > Errol Lewars > ==== > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: elewars@alchemy.chem.utoronto.ca > -- Original Sender From: Address: elewars@alchemy.chem.utoronto.ca > 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 >