From mbeck@oci.unizh.ch Thu Aug 6 02:13:23 1998 Received: from rzusuntk.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id CAA16433 Thu, 6 Aug 1998 02:13:22 -0400 (EDT) Received: [from rzurs10.unizh.ch (mbeck@rzurs10.unizh.ch [130.60.68.60]) by rzusuntk.unizh.ch (8.8.5/SMI-5.25) with ESMTP id IAA05704; Thu, 6 Aug 1998 08:13:20 +0200 (MET DST)] Received: from localhost (mbeck@localhost) by rzurs10.unizh.ch (AIX4.2/UCB 8.7/8.7) with SMTP id IAA124308; Thu, 6 Aug 1998 08:13:19 +0200 (MEST) X-Authentication-Warning: rzurs10.unizh.ch: mbeck owned process doing -bs Date: Thu, 6 Aug 1998 08:13:19 +0200 (MEST) From: "Michael E. Beck" To: computational chemistry mailing list Subject: Re: CCL:Off-diagonal elements of the CI matrix In-Reply-To: <9808051719.ZM19286@hathi.chem.pitt.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 5 Aug 1998, Gustavo Moura wrote: > Dear CCL readers, > I am writing a program to do CI calculations on some conjugated > molecules using semiempirical (PPP) parameters. Unfortunately, I am having > problems to calculate the off-diagonal elements of the CI matrix. In their book > Szabo e Ostlund show (tables 2.3 and 2.4) how to calculate these elements when > the determinants are in maximum coincidence. I am looking for references where > I Dear Sir, maybe this not quite the answer you are expecting, but from your letter i suspect that your program is in a very early stage of development. A very elegant way to set up the Hamiltonian in a basis of spin adapted configurations (CCFs) is to use the graphical approach pioneered by Paldus and Shavitt, GUGA. This approach also gives a very smooth way to construct the configuration space. GUGA seems to be applied mainly in ab initio theory, but personally i think it's very well suited for semiempirics, too. Once you have got used to the graphs, you'll love them, promise. Coming back to your question: In GUGA problems like "maximal coincidence" just do not arise. sincerly Michael E. Beck ___________________________________________________________________ Dr. Michael E. Beck | privat: Organisch--Chemisches Institut | Zschokkestr. 12a Theoretische Gruppe, Prof. W. Thiel | CH--8037 Zuerich Universitaet Zuerich | +41-1-271 54 39 Winterthurerstr. 190 |___________________________ CH--8057 Zuerich Tel.: +41-1-635-6117 web : www.unizh.ch/~mbeck Fax.: 6836 mail: mbeck@unizh.ch ___________________________________________________________________ From srk@engc.bu.edu Thu Aug 6 10:58:19 1998 Received: from engc.bu.edu (xmw39ACBuQdV2acrwV895n5Z5WLBuzYS@ENGC.BU.EDU [128.197.185.241]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA19245 Thu, 6 Aug 1998 10:58:19 -0400 (EDT) Received: (from srk@localhost) by engc.bu.edu ((8.8.8.buoit.b4)/8.8.8/(BU-W-06/24/98-b7)) id KAA10963; Thu, 6 Aug 1998 10:58:19 -0400 (EDT) From: "S. Roy Kimura" Message-Id: <199808061458.KAA10963@engc.bu.edu> Subject: Summary: TINKER vs CHARMm To: chemistry@www.ccl.net Date: Thu, 6 Aug 1998 10:58:19 -0400 (EDT) Cc: srk@engc.bu.edu X-Mailer: ELM [version 2.4ME+ PL19 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hello, here is a summary of responses I received for my question I posted a few weeks ago. Thank you very much for all the advice and comments Roy ----- S. Roy Kimura Molecular Engineering Research Laboratory Department of Biomedical Engineering Boston University email: srk@bu.edu phone: (617)353-4697 ----------------------< original question >------------------------ Dear CCLers, Recently, I have been thinking about using the TINKER package (by Jay Ponder) rather than CHARMm since TINKER's source looks much easier to modify. As a check, I decided to calculate the internal energy of a 9 residue peptide in vaccuum using both the CHARMm and TINKER programs. However, I have been getting rather different energies even though I used the same parameter sets and identical coordinates (for TINKER, I used the charmm.prm file supplied with the TINKER distribution which is supposed to be equivalent to CHARMm22 parameters). Does anyone have any idea what the problem might be? Roy ------------------------------------------------------------------- Dear Dr. Kimura: I recently tested TINKER on a simple MD simulation of liquid argon. The calculated kinetic energy does not correspond to the temperature of the simulation. There are no obvious reasons for the error in the TINKER results). Hubert ------------------------------------------------------------------- Roy, I've worked with a number of different force fields in different packages, so I can offer a few suggestions. However, since I have not worked with either package, I cannot comment specifically. 1) Check to see that the forcefields are defined exactly the same. The program may say that it uses the same forcefield, but it could have been modified slightly. This happens all the time with peptides, because everyone is interested in getting the best result. (Ex. Improper torsional restraints may be used in one program to hold the peptide bond flat, but this may not be the case in the other program.) 2) Check to see that the parameters are compatible as is. In other words, check to make sure that they don't need to be divided by 2 or something simple like that. Also, some programs make you enter the non-bonded parameters as sigma, epsilon, while others have you enter them a different way. You said that you used a compatible parameter set, but is it possible that it came from a different version of the program? Sometimes authors change these things while they continue to improve their software. 3) Try a simple case like ethane or butane. If you are still getting different values, then drop back to methane or similar without 1,4 interactions. 4) Check to see that dielectric constants, H-bond functions, and such are turned on/off the same way in both programs. Alos, the non-bonded cutoffs (if used) should be defined and set to the same value in both programs. 5) Double precision vs. Single precision. You said the coordinates were the same, but do the packages both use double precision throughout? This would only account for very slight differences, but it is something to keep in mind. 6) I really hate to say this, but if all else fails, trust the package that has been around the longest. Good luck. Trust me, I know how frustrating it came be to find these errors. David Maxwell Senior Scientist Texas Biotechnology Corp. 7000 Fannin, Suite 1920 Houston, TX 77584 E-Mail: dmaxwell@tbc.com Phone: (713) 796-8822 x102 ------------------------------------------------------------------- Dear Roy Kimura, I just returned from some time away from St. Louis and saw your post to CCL about "TINKER vs. CHARMm". I would be extremely interested in resolving (or at least rationalizing) the differences you are seeing between energies computed with our charmm.prm parameters and whatever CHARMm22 parameters you are using with "real" CHARMm. There are several possibilities. First, "charmm22" means different things to different people, MSI put out a version of charmm22 parameters, and Alex MacKerrell put out several versions over many years that were all loosely called "charmm22". The charmm.prm provided with TINKER is a translation to TINKER format of a version of charmm22 distributed with the related XPLOR package from Axel Brunger as of about mid-1994. At the time we compared energies from TINKER's charmm.prm with the corresponding XPLOR calculation, and got very close, but not "perfect" agreement for various polypeptide tests. The "official" paper on the protein parameters for charmm22 has just been published (J Phys Chem, 102, 3586-3616, 1998). We certainly intend to update TINKER to this latest version of charmm22 and validate vs. the tests reported in this article, but we have not yet found time to do so. I would rather expect that the differences between the new "official" parameters and our older ones would be "small" (but not necessarily insignificant...). If you are instead getting "large" differences between TINKER and CHARMm, then the problem may lie elsewhere. Several people have caused themselves trouble by mixing parameter sets from one version of TINKER with source code and/or executables from another. This can lead to very odd results since we have frequently made changes to both parameter file formats and the code that are not "backward compatible". Regardless you should test with the most recent version of TINKER (currently 3.6). As a relatively new package, TINKER has undergone a large number of bug fixes as it has come into somewhat wider use. Also we have corrected mistranslations in our charmm.prm as they have cropped up (our charmm.prm was originally generated manually!). I know that some fairly early versions of TINKER were floating around BU Biomed. Engineering. Of course it is still possible that we have a "bug" in our implementation of the charmm function, but I tend to think we have things right at this point. Perhaps the best way to proceed, would be for you to send me the input and output files you are using for CHARMm (with as much detail as possible turned on for individual energy terms in the output). I'll take a look and see if I can't quickly find the origin of your trouble. Obviously, I'm very interested in seeing that TINKER reproduces charmm (and all the other force fields we support) as accurately as possible. Jay Ponder -------- Jay W. Ponder Phone: (314) 362-4195 Biochemistry, Box 8231 Fax: (314) 362-7183 Washington University Medical School 660 South Euclid Avenue Email: ponder@dasher.wustl.edu St. Louis, Missouri 63110 USA WWW: http://dasher.wustl.edu/ ------------------------------------------------------------------- THIS IS MY RESPONSE TO DR. PONDER'S POST Dear Professor Ponder, Since I posted that message, I experimented with different "charmm22" parameter sets, and found a set that gave charmm results very close to those from TINKER -- that is the charmm22 parameters that I downloaded from Axel Brunger's X-PLOR website (called top_all22_prot_b4.inp and par_all22_prot_b4.inp). In my initial test, I used the all atom "charmm22" parameters supplied with MSI, which, according to some people, is known as charmm19 parameters, despite the fact that it says charmm22 in the beginning of the file. However, when I say very close, it means that it is much closer than what I had been seeing when I used the MSI parameters -- but there are some differences as you mentioned. Here are snippets from the outputs of both programs: ...................................................................... Total Potential Energy : -40.4963 Kcal/mole Energy Component Breakdown : Kcal/mole Interactions Bond Stretching 18.2026 135 Angle Bending 23.3052 244 Urey-Bradley 1.8769 112 Improper Dihedral 0.1833 17 Torsional Angle 46.8472 362 1-4 van der Waals 89.1869 346 Other van der Waals -10.2909 7921 Charge-Charge -209.8075 7787 ...................................................................... ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -36.49659 0.00000 10.32686 ENER INTERN> 16.88385 26.02777 1.56513 38.97038 0.18396 ENER EXTERN> 91.72723 -211.85492 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- ...................................................................... The above are the energy calculations from a single conformation of a 9 residue peptide 2VAB (PHE ALA PRO GLY ASN TYR PRO ALA LEU). In both cases, I used the identical coordinates (same pdb file) which I created using charmm after minimizing the crystal structure by 50 steps. TINKER calculations were done with the latest version that I just recently downloaded (ver 3.6). In the TINKER keyfile, I have set the 1-4 scaling factor to 2.0 since that is what I understand charmm does with 1-4 nonbonded interactions. It appears the largest discrepancies lie in the torsional and Van der Waals energies (I presume one adds your '1-4' and 'other VdW' to get the equivalent of charmm's 'VDWaals'). Do you have any ideas as to why these discrepancies exist? From rino@gpc.ibc.wustl.edu Thu Aug 6 11:33:32 1998 Received: from wugate.wustl.edu (wugate.wustl.edu [128.252.120.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA19695 Thu, 6 Aug 1998 11:33:31 -0400 (EDT) Received: from [128.252.137.150] ([128.252.137.150]) by wugate.wustl.edu (8.8.8/8.8.5) with ESMTP id KAA23267 for ; Thu, 6 Aug 1998 10:33:29 -0500 (CDT) Date: Thu, 6 Aug 1998 10:33:29 -0500 (CDT) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: Rino Ragno Subject: GAMESS -> TURBOMOLE Hi to everyone, I am looking for a preogramm to convert the gamess output file into turbomole format. Is out there anyone that can help in this? Thanks in advance. Ciao -- Rino Ragno ++----------------------------------------------------------------------++ ++----------------------------------------------------------------------++ || || || Dr. Rino Ragno E-mail: ragno@uniroma1.it || || Institute for Biomedical Computing or: rino@gpc.wustl.edu || || Center for Molecular Design or: ragno@axcasp.caspur.it || || Box8036, Washington University Phone : 314-362-2272 || || 700 South Euclid Avenue FAX : 314-362-0234 || || St. Louis, Missouri 63110 || || U. S. A. || || || || WEB PAGE : www.ibc.wustl.edu/cmd/people/rino/rino.html || || || ++----------------------------------------------------------------------++ ++----------------------------------------------------------------------++ From haney@netcom.com Thu Aug 6 19:11:18 1998 Received: from netcom15.netcom.com (haney@netcom15.netcom.com [192.100.81.128]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA22790 Thu, 6 Aug 1998 19:11:17 -0400 (EDT) Received: (from haney@localhost) by netcom15.netcom.com (8.8.5-r-beta/8.8.5/(NETCOM v1.02)) id QAA20851; Thu, 6 Aug 1998 16:11:18 -0700 (PDT) From: "Dr. David N. Haney" Message-Id: <199808062311.QAA20851@netcom15.netcom.com> Subject: Software for Hydrophobicity, Indices, 3D Lattice To: CHEMISTRY@www.ccl.net Date: Thu, 6 Aug 1998 16:11:17 -0700 (PDT) Reply-To: haney@hbond.com X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit eduSoft, LC provides unique computational chemistry functionality interfaced to standard molecular modeling packages (Insight, Sybyl, Chem-X). HINT is a standard in logP and hydrophobicity and hydropathic interactions evaluation. Molconn-Z is a standard for generating molecular indices used for QSAR. A new program HASL, will become available shortly that offers unique 3D lattice functionality for QSAR problems. HINT ################### -calculates logP and graphs 3D hydrophobicity: useful in drug database screens -constructs complementary maps of hydrophobicity: useful to refine drug design -contains functionality for scoring and visualizing ligand/inhibitor docking -calculates errors in PBD structures and predicts stability of mutants Molconn-Z ############## -calculates molecular connectivity, shape, e-state, and information indices -environment allows data to be used with PLS, component and other analyses -useful for similarity analysis in database searching HASL ################### -deconvolutes complex 3D problem by assigning values to a 3D lattice -used in 3D QSAR for DHFR, glutamine syntase, HIV protease -useful in analysing experimental data and predicting results of new drugs For more information please contact me, Dr. David N. Haney, at haney@hbond.com, or take a look at the web site #### http://www.eslc.vabiotech.com/ #### -- ************** David N. Haney, Ph.D. ******************** * Haney Associates Phone - 206-232-1401 * * 4212 93rd Ave SE FAX - 206-236-5268 * * Mercer Island, WA 98040 Email - haney@hbond.com * * * ************** http://www.hbond.com/ ******************** From adam@cherwell.com Fri Aug 7 10:59:28 1998 Received: from congo.cherwell.com (congo.cherwell.com [193.82.249.202]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA27412 Fri, 7 Aug 1998 10:59:27 -0400 (EDT) Received: from wharfe.cherwell.com ([193.82.249.214]) by congo.cherwell.com (Post.Office MTA v3.1.2 release (PO205-101c) ID# 0-0U10L2S100) with SMTP id AAA461 for ; Fri, 7 Aug 1998 15:59:22 +0100 Message-Id: <3.0.5.32.19980807155910.0086b100@cherwell.com> X-Sender: adam@cherwell.com X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Fri, 07 Aug 1998 15:59:10 +0100 To: chemistry@www.ccl.net From: Adam Hodgkin Subject: Ideas for using a Chemistry Whiteboard Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Internet Chemist, ChemWeb asked Cherwell Scientific to give a virtual lecture on JavaBeans for Chemistry which is now on the ChemWeb site. See extract from their announcement, below. The most interesting thing about this lecture was the Chemistry Whiteboard which VEI had put together from the ChemSymphony Beans (VEI specialise in organising electronic conferences and manage the lecture series). We think they have some cool ideas about how to use Beans interactively. Take a look at it if you want to get a 'feel' for what a Java chemistry Whiteboard can do. Once you have looked at it, you may want to ask a colleague to join you in a sketching session at the Virtual Whiteboard. Using the Whiteboard leads to speculation about possible developments. If you have ideas about specific 'must have' applications for a chemistry WhiteBoard reply direct to me or to this list. We offer a Magnum of champagne (or equivalent present) to the best idea submitted and I will produce a summary of replies received for the list. > ChemSymphony Beans Demonstration Open > >The ChemSymphony whiteboard is now accessible to all ChemWeb 7 registrants >in the auditorium at http://chemweb.vei.co.uk. This demo allows you to >create and modify a structure in real time, and display it to other >delegates who are logged in. To use the demo, you must have either >Internet Explorer 4 or the Java plugin (Win 95/NT/Solaris) with Netscape 3 >or 4. For information about the Java plugin, see http://java.sun.com/products/plugin/index.html. Best wishes Adam --- --- Adam Hodgkin | e-mail: adam@cherwell.com Chairman | Phone: +44 (0)1865 784810 Cherwell Scientific Publishing | Fax: +44 (0)1865 784801 Oxford OX4 4GA, UK | URL: http://www.cherwell.com --- --- From ihtrap@hotmail.com Fri Aug 7 17:57:40 1998 Received: from hotmail.com (f115.hotmail.com [207.82.250.165]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id RAA01651 Fri, 7 Aug 1998 17:57:40 -0400 (EDT) Received: (qmail 29565 invoked by uid 0); 7 Aug 1998 21:57:11 -0000 Message-ID: <19980807215711.29564.qmail@hotmail.com> Received: from 128.102.199.140 by www.hotmail.com with HTTP; Fri, 07 Aug 1998 14:57:11 PDT X-Originating-IP: [128.102.199.140] From: "Artiben Taylor" To: chemistry@www.ccl.net Subject: permittivity Content-Type: text/plain Date: Fri, 07 Aug 1998 14:57:11 PDT CCLers: In the expression for Coulombic potential e^2 V(r) = - ----------- 4 pi Eo r where Eo the permittivity of free space; e charge; r distance between electron and proton. Could someone enlighten me the significance of permittivity, what actually it means and why does the coulombic potential decreases with the increase in permittivity. Thanks Artiben ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From plyne@bellatrix.pcl.ox.ac.uk Sat Aug 8 09:31:27 1998 Received: from oxmail4.ox.ac.uk (oxmail4.ox.ac.uk [163.1.2.33]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id JAA03514 Sat, 8 Aug 1998 09:31:26 -0400 (EDT) Received: from bellatrix.pcl.ox.ac.uk by oxmail4 with SMTP (PP); Sat, 8 Aug 1998 14:31:19 +0100 Received: from localhost by bellatrix.pcl.ox.ac.uk via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for id OAA11370; Sat, 8 Aug 1998 14:12:30 +0100 Date: Sat, 8 Aug 1998 14:12:29 +0100 (BST) From: Paul Lyne Sender: plyne@bellatrix.pcl.ox.ac.uk To: chemistry@www.ccl.net Subject: g94 and alphas Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi I am trying to get g94 to run on an alpha that has RedHat Linux as the operating system. Has anyone managed to compile this with the gnu compiler OR compiled it on a DEC machine and got the executable to run on an alpha using linux. Thanks for your help. Paul --------------------------------------------------------------------------- Dr. Paul D. Lyne Department of Chemistry Tel: +44 1865 275932 New Chemistry Laboratory Fax: +44 1865 275905 South Parks Road Oxford, OX1 3QT paul.lyne@chem.ox.ac.uk United Kingdom --------------------------------------------------------------------------- From tapas@risky3.thchem.siu.edu Mon Aug 10 13:20:48 1998 Received: from risky3.thchem.siu.edu (risky3.thchem.siu.edu [131.230.89.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA12871 Mon, 10 Aug 1998 13:20:45 -0400 (EDT) Received: from localhost (tapas@localhost) by risky3.thchem.siu.edu (AIX4.2/UCB 8.7/8.7) with SMTP id MAA17988 for ; Mon, 10 Aug 1998 12:26:32 -0500 (CDT) Date: Mon, 10 Aug 1998 12:26:26 -0500 (CDT) From: Tapas Kar To: "Comp. Chem. List" Subject: Problem with O3 freq. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everybody, Here is the expt vib. frequencies of O3 705 1110 and 1042 ( Ref. Herzberg ) Theoretical values are (output of mp2(full)/6-31+G*) A1 A1 B2 Frequencies -- 725.8632 1162.4426 2391.7224 Red. masses -- 15.9949 15.9949 15.9949 Frc consts -- 4.9653 12.7343 53.9081 IR Inten -- 6.5303 2.4236 1635.3846 In fact we tried with other basis sets like 4-31G, 6-311G* at MP2 level and the values are close to the above values. Clearly 2391 (B2 mode) is too high. what is the problem here. Tapas ~ -------------------------------------------- Tapas Kar, Ph. D Asst. Scientist/Asst. Professor (Adjunct) Forestry Bldg 118 Department of Chemistry Southern Illinois University at Carbondale Illinois 62901-4409 Fax: (618) 453 6408 Tel: (618) 453 6433(Lab) 6485(Office) -------------------------------------------- From dspellmeyer@combichem.com Mon Aug 10 15:48:39 1998 Received: from hermes.combichem.com (hermes.combichem.com [207.158.48.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA14721 Mon, 10 Aug 1998 15:48:39 -0400 (EDT) Received: from karpo.info.combichem.com ([207.158.46.85]) by hermes.combichem.com (Post.Office MTA v3.1.2 release (PO205-101c) ID# 0-49457U200L100S0) with SMTP id AAA327 for ; Mon, 10 Aug 1998 12:44:32 -0700 Message-Id: <3.0.5.32.19980810125100.00800d70@mail.combichem.com> X-Sender: dspellmeyer@mail.combichem.com X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32) Date: Mon, 10 Aug 1998 12:51:00 -0700 To: CHEMISTRY@www.ccl.net From: dspellmeyer@combichem.com (David Spellmeyer) Subject: Call for Papers - Anaheim ACS Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Second and Final Announcement SYMPOSIUM ANNOUNCEMENT AND CALL FOR PAPERS Applications of Computers in Combinatorial Chemistry to be held at the American Chemical Society Meeting in Anaheim, CA March 21-25, 1999 Sponsored by the Division of Computers in Chemistry This symposium will cover all aspects of computational chemistry applied to the field of molecular diversity and combinatorial chemistry. This includes design and analysis of combinatorial libraries, design of conformationally constrained libraries, computational measures of diversity, information-based libraries, coverage-based libraries, and others. New algorithms and applications of existing algorithms are welcome. The due date for 150 word abstracts is November 18, 1998. For planning purposes, however, please let me know if you plan to submit an abstract no later than August 15, 1998. David Spellmeyer CombiChem, Inc. 1804 Embarcadero Road, Suite 201 Palo Alto, CA 94306 (650)-842-0560 ext. 105 (650)-842-0575 FAX dspellmeyer@combichem.com http://www.combichem.com From r40757@email.mot.com Mon Aug 10 22:02:53 1998 Received: from spsem02.sps.mot.com (spsem02.sps.mot.com [192.70.231.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id WAA18147 Mon, 10 Aug 1998 22:02:52 -0400 (EDT) Received: from mogate.sps.mot.com by spsem02.sps.mot.com (4.1/SMI-4.1/Email 2.1 10/25/93) id AA14197 for chemistry@www.ccl.net; Mon, 10 Aug 98 19:02:46 MST Received: from emailsps.sps.mot.com by mogate.sps.mot.com (4.1/SMI-4.1/Email-2.0) id AA02471 for watts@qtp.ufl.edu; Mon, 10 Aug 98 19:02:44 MST Received: from email.mot.com (zkorkin [223.189.20.185]) by sps.mot.com (8.8.6 (PHNE_14041)/8.8.6) with ESMTP id TAA17408; Mon, 10 Aug 1998 19:02:43 -0700 (MST) Sender: korkin@act.sps.mot.com Message-Id: <35CFA7CD.9816542C@email.mot.com> Date: Mon, 10 Aug 1998 19:09:17 -0700 From: Anatoli Korkin X-Mailer: Mozilla 4.05 [en] (X11; I; IRIX64 6.4 IP30) Mime-Version: 1.0 To: Tapas Kar , CCL , Rod Bartlett , watts@qtp.ufl.edu Subject: Re: CCL:Problem with O3 freq. References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Tapas, The problem is that for highly correlated systems like O3, for example, MP2 (or MBPT[2]) is not "the word from Bible". You need to apply coupled cluster (see Watts & Stanton & Bartlett, CPL, 1991, 178, p. 471) or multi-reference methods to get correct results. To find out when you may get "a trouble" look at LUMO energy, and if it is negative the system is highly correlated. You may also see that your IR intensity is unrealistically high, which shows that perturbation theory is not working "properly". Chemical systems, which are "under suspition" for high correlation effects are: 1) electron rich systems; 2) transition states; 3) system with "unusual" coordination numbers; 4) unique Lewis structure can not be drawn; 5) condensed multiple bonds; 6) radicals and biradicals. Of course, many systems fall into a few categories. Anatoli P.S. B3LYP is not so bad after all in this case even it is about or even faster than MP2. At least you get them in a right order (B3LYP/6-31+G*): A1 B2 A1 Frequencies -- 733.1291 1220.1424 1257.5397 Red. masses -- 15.9949 15.9949 15.9949 Frc consts -- 5.0652 14.0299 14.9031 IR Inten -- 6.3178 232.6091 .0020 Raman Activ -- .0000 .0000 .0000 Depolar -- .0000 .0000 .0000 With CCSD (which is more expensive) you get 748, 1240 and 1256 (Stanton et al, JCP, 1989, 90, p. 1077. Regards, Anatoli Tapas Kar wrote: > > Hi everybody, > > Here is the expt vib. frequencies of O3 > 705 1110 and 1042 ( Ref. Herzberg ) > Theoretical values are (output of mp2(full)/6-31+G*) > A1 A1 B2 > Frequencies -- 725.8632 1162.4426 2391.7224 > Red. masses -- 15.9949 15.9949 15.9949 > Frc consts -- 4.9653 12.7343 53.9081 > IR Inten -- 6.5303 2.4236 1635.3846 > > In fact we tried with other basis sets like 4-31G, 6-311G* at MP2 level > and > the values are close to the above values. > Clearly 2391 (B2 mode) is too high. what is the problem here. > Tapas > ~ > > -------------------------------------------- > Tapas Kar, Ph. D > Asst. Scientist/Asst. Professor (Adjunct) > Forestry Bldg 118 > Department of Chemistry > Southern Illinois University at Carbondale > Illinois 62901-4409 > > Fax: (618) 453 6408 > Tel: (618) 453 6433(Lab) 6485(Office) > -------------------------------------------- > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: tapas@risky3.thchem.siu.edu > -- Original Sender From: Address: tapas@risky3.thchem.siu.edu > 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 -- ****************************************************************** Anatoli A. Korkin, Ph.D Predictive Engineering Lab Computational Chemist Semiconductor Products Sector Motorola Inc., MD M360 Tel: (602) 655-3171 2200 W. Broadway Road Fax: (602) 655-5013 Mesa AZ 85202 E.mail: r40757@email.mot.com *******************************************************************