From pis_diez@cpd.uva.es Wed Apr 14 13:05:42 1993 Date: Wed, 14 Apr 1993 13:05:42 UTC+0100 From: Reinaldo Pis Diez Subject: Re:Looking for Xalpha program To: chemistry@ccl.net (confirm) Message-Id: Hi all netters!! Two weeks ago I posted a mail to the list looking for an Xalpha code (free if possible). I received mails from many people interested in the code (if available): Stephen Urquhart; Nelson Morgon, from Campinas; Tony Duben,from St. Louis; Katrina Werpetinski; Steve Cook, from Berke- ley and Paul Edwards, from Edinboro. Unfortunately, I received only one answer to my post: Dr. Raul Cachau, from the National Cancer Research Institue at Frederick, who stated that an Xalpha code, XASW 2.0, is available at QCPE under the number 465. It's got a 14000-lines code and cost ca. u$s 400. That's all. Regards, Reinaldo ********************************************************************* * Dr. Reinaldo PIS DIEZ * Tel: +34 83 42 31 47 * Department of Theoretical Physics * FAX: +34 83 42 30 13 * Faculty of Sciences * E-mail: pis_diez@cpd.uva.es * 47011 Valladolid, Spain * * ********************************************************************* From 21NBCJ@npd1.ufpe.br Wed Apr 14 06:59:00 1993 Date: Wed, 14 Apr 1993 09:59 -0300 From: Nivan Bezerra <21NBCJ@npd1.ufpe.br> Subject: one- and two-center electron integral over STO To: chemistry@ccl.net Message-Id: <01GWZWZP43LC000264@NPD1.UFPE.BR> Dear Networks friends, Does anyone know any reference about analytical algorithm for one- and two-center electron integral over Slater Type Orbitals? Thank you in advance for the help. Sincerely Nivan Bezerra da Costa Jr. Departamento de Quimica Fundamental -UFPE Recife - PE - Brazil E-mail: 21nbcj@npd1.ufpe.br or nivan@vaxdqf.ufpe.br From ngo@tammy.harvard.edu Wed Apr 14 06:15:36 1993 Message-Id: <9304141415.AA29313@tammy.harvard.edu> To: Ramon Garduno Subject: Re: Looking for MM2/MM3 software. Date: Wed, 14 Apr 93 10:15:36 -0400 From: ngo@tammy.harvard.edu Two days ago, Ramon Garduno wrote: ramon> I am in the process of publishing a paper, but a reviewer suggested ramon> to perform some calculations on the molecules I report with either ramon> MM2(87) or better yet MM3. However, I do not have access to any of ramon> them. ramon> ramon> Does any body knows where I can put my hands unto these programs? ramon> If they are from public sources, it will be appreciated. I posted precisely the same request some months ago. As it turned out, my only option was to order from QCPE. MM2(87) costs $150; MM2(91) costs $400. I do not know how much MM3 costs. I purchased a copy of MM2(87). The only form in which it comes is a VAX copy tape. You might need to do a little bit of computational gymnastics to read the VAX tape. QCPE is the Quantum Chemistry Program Exchange at Indiana University. Contact: Quantum Chemistry Program Exchange Creative Arts Building 181 Indiana University Bloomington, Indiana 47405 U.S.A. (812) 855-4784 Hope this helps, --Tom Ngo ngo@tammy.harvard.edu From gawboy@sodium.mps.ohio-state.edu Wed Apr 14 06:44:00 1993 Date: Wed, 14 Apr 93 10:44:00 EDT From: Galen Gawboy Message-Id: <9304141444.AA01213@sodium> To: chemistry@ccl.net, h8714031@hkuxa.hku.hk Subject: Re: Question on Dynamic Electron Correlation. Everybody, > Dear Sir, > > I am interesting in MCSCF calculation as most text mentioned that MCSCF is > good in treating near degeneracy effect but still cannot deal with the > dynamical correlation effect. I would like to know what is dynamical correlation > effect? What is the physical meaning? Any suggested reading? > I am sure this question will generate numerous responses, and I am looking forward to seeing what other people have to say on this subject, but I can't resist the urge to open my big mouth. My view of dynamic correlation is that it is the energy lowering obtained by accounting for the fact that like charges repel each other. In an MCSCF calculation, this is only partially accounted for. If you were to do a complete active space mcscf calculation which included every single orbital in your basis set, you would get results identical with a full ci calculation, ( of course in practice it might be challenge to get it to converge). If this is what you wanted to do, it would be more efficient to do a full ci calculation. The mcscf procedure is roughly as follows: -1. An active space is chosen. This is typically a relatively small fraction of the total number of MO's available. For example in a calculation of the benzene cation only the pi and pi* orbitals would be included. -2. Within this active space a full ci calculation is performed. -3. These approximate eigenstates are then used to construct the orbital and state gradient vectors, and the orbital, state, and orbital state coupling matrices. -4. The information obtained in part 3 is used to construct the transformation matrix which is used to transform the orbitals for the next iteration. -5. If the orbital and energy change is less than the convergance criteria the calculation is done, other wise go back to 1. In this example problem, you may notice that a full ci calculation is performed in the pi space every single iteration, yet the mcscf procedure is called a non-dynamic treatment of electron correlation. The reason for this is that only the highest lying orbitals were correlated. These orbitals are the most diffuse orbitals in the benzene cation, and for these orbitals dynamic correlation is the least important. There is more stabilization to be gained by accounting for the fact that the electrons in the sigma orbitals will try to stay as far away from each other as possible. An interesting discussion of this issue can be found in Jorgenson and Simon's book Second Quantized Based Methods in Quantum Chemistry. They treat the MCSCF and MRCISD methods in a unified fashion. A good reference on the MCSCF method would be: Ron Shepard, Advances in Chemical Physics-II, Volume LXVII,page 64-199. A nice statement of the dynamic electron correlation problem is: P.O. Lowdin, Advances in Chemical Physics, Volume II: 207. Some good entry points to the literature of dynamic electron correlation are: Szabo and Ostlund, Modern Quantum Chemistry. Mcweeny and Sutcliffe, Molecular Quantum Mechanics. Hope this is helpful. -Regards Galen .sigs are for management stoolies. From YUAN%UCCHEM@UCBEH.SAN.UC.EDU Wed Apr 14 07:30:01 1993 Date: Wed, 14 Apr 1993 11:30:01 -0400 (EDT) From: "JIE YUAN, CHEMISTRY, U. CINCINNATI" Subject: RMS comparison -- Discover (Biosym) To: chemistry@ccl.net Message-Id: <01GWZZ664SF68WWQJQ@UCBEH.SAN.UC.EDU> Hi, Netters! I am using the standalone version of Discover (2.8) to do an RMS comparison. I followed the examples provided in the manual but could not get the calculation running. The error message in the .out file are two kinds: (1) a number of residues (e.g. ALA 7) appear twice in the template file; (2) cannot open template file "xxxx.ttt". I would appreciate it if you can show be a typical input file of yours that would make a run. The rest of this posting will go into details of my problem. The purpose is to compare the minimized structure with the starting structure. I have complete files for both of them (i.e. .car, .mdf, etc.) and have tried to name one of the structures as the "template". I prefer to use the starting structure as the template though. Both structures have the same number of atoms and connectivity list. In starting the calculation with the standalone Discover, I need a .inp file that is associate with .car and .mdf of one of the structures. I then included a sentence to read a template file, which is the other structure of the interest. So far, I have always failed within 1 minute after launching the calculation (indicated in the .out file). It seems that the initial step was successful in reading in the structure that has the same name as the .inp. The .out file showed no complaint until after the command line that reads the template file by its name. Here I should mention that I am putting the .car file of the other structure as the template file name (in the .inp file command line). Then, the .out file says "unable to read template file xxxx.yyy". My hope is that if some of you let me see your input files, I probably can figure out what I should do to make it work. I can certainly show you my .inp and .out files so that you know what is wrong with my approach. Let me know if you are interested. Regards, Jie Yuan (513)556-9230 From DSMITH@uoft02.utoledo.edu Wed Apr 14 07:31:59 1993 Date: Wed, 14 Apr 1993 12:31:59 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: second call for posters To: chemistry@ccl.net, mmodinfo@uoft02.utoledo.edu, hyperchem@autodesk.com Message-Id: <01GX029L1IQA003QZ1@UOFT02.UTOLEDO.EDU> SECOND CALL: (Note that some money for graduate students is still available.) The Computers in Chemistry Division of the ACS is sponsoring a symposium entitled "Modeling the Hydrogen Bond" which will run for two full days at the Chicago meeting in August (22nd - 27th). We have approximately 25 speakers, and the sessions will be set up along the general lines of Methodology, Organic, and Biochemistry. We are now soliciting posters for this symposium. Posters may be put into a special session, the general division poster session, or possibly Sci-Mix. Submissions by graduate students are especially solicited. In fact, up to 10 graduate students will be eligible for reimbursement of travel and associated costs up to $300. To submit: Please send one (1) copy of your abstract on the standard ACS abstract form to me at the address listed below by April 25th, 1993. Faxed submissions are acceptible ONLY if an original is also sent in time to meet the deadline. Graduate students: If you wish to apply for travel funds, please attach a separate letter to your abstract with a short justification why you should receive the funds. We are looking forward to a great symposium. I hope to see you all there! Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From imtvi06@cc.csic.es Wed Apr 14 23:03:19 1993 Date: Wed, 14 Apr 1993 23:03:19 UTC+0100 From: Luis Montero Subject: Molec. Dynamics for Olygosacharides To: chemistry@ccl.net (confirm) Message-Id: <296*/S=imtvi06/OU=cc/O=csic/PRMD=iris/ADMD=mensatex/C=es/@MHS> Dear netters: We are carrying out theoretical research on conformations and hydration of oligosacharides as tropical disease antigens. This oligosacharides are tri- or tetrasacharides in the external membrane of extrange cells. We need a public domain FORTRAN code of a program to perform molecular dyna- mical modelings of hydration and its effect in conformations. We have already performed extensive semiempirical MO calculations on orbital steric effects and conformational analysis. But it only goes to gas phase models, far from the serum reality. Thank you, very much in advance. Luis Montero Universidad de La Habana, Cuba CSIC, Madrid From hogue@canada.den.mmc.com Wed Apr 14 10:35:18 1993 Date: Wed, 14 Apr 93 16:35:18 MDT From: hogue@canada.den.mmc.com (Pat Hogue 1-2183) Message-Id: <9304142235.AA00401@canada.den.mmc.com> To: chemistry@ccl.net Subject: Perfluorodimethyl ether I keep getting an excessivly long C-F bond length for one of the bonds on either end of perfluorodimetyl ether usinf AM1. Can anyone offer an explaination? Thanks in advance. From d3f012@gator.pnl.gov Wed Apr 14 08:54:26 1993 Date: Wed, 14 Apr 93 15:54:26 PDT From: d3f012@gator.pnl.gov Subject: Atomic charges in Discover To: chemistry@ccl.net Message-Id: <9304142254.AA07176@gator.pnl.gov> Can anyone tell me how the atomic charges in the Consistent Valence Force Field (cvff) are obtained? I have not found any specifics in the literature yet. Mark Thompson ************************************************************************** Mark A. Thompson Sr. Research Scientist email: d3f012@pnlg.pnl.gov Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory voice: 509-375-6734 PO Box 999, Mail Stop K1-90 Richland, WA. 99352 Argus available via anonymous ftp from pnlg.pnl.gov (130.20.64.11) (in the argus directory). Download the README file first. Disclaimer: The views expressed in this message are solely my own and do not represent Battelle Memorial Institute, Pacific Northwest Laboratory, or any of its clients. **************************************************************************