From owner-chemistry@ccl.net Thu Nov 2 03:32:09 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id DAA27135; Thu, 2 Nov 1995 03:20:05 -0500 Received: from chemul.uni.lodz.pl for pitsel@chemul.uni.lodz.pl by bedrock.ccl.net (8.7.1/950822.1) id DAA09331; Thu, 2 Nov 1995 03:19:26 -0500 (EST) Received: by chemul.uni.lodz.pl (5.65/25-eef) id AA18481; Thu, 2 Nov 95 08:19:12 +0100 Message-Id: <9511020719.AA18481@chemul.uni.lodz.pl> From: pitsel@chemul.uni.lodz.pl (Piotr Seliger) X-Mailer: SCO System V Mail (version 3.2) To: chemistry@ccl.net, jlye@tx.ncsu.edu, m.t.cronin@livjm.ac.uk, moralega%a1@lldmpc Subject: summary AM1 vs PM3 Date: Thu, 2 Nov 95 8:19:11 MEZ This is the summary of the responses I got to my request about AM1 vs PM3 references. Thanks for help. ---------------- ***************************************************************************** Dear Dr. Seliger, Following is a note that I sent to the next over a year ago. Perhaps it will be informative. Our SAM1 papers also extensively documented PMs vs AM1 as well as SAM1. The references for these are: 1. Dewar, M. J. S.; Jie, C.; Yu, G. Tetrahedron 1993, 23, 5003. 2. Holder, A. J.; Dennington, R. D.; Jie, C. Tetrahedron 1994, 50, 627. 3. Holder, A. J.; Evleth, E. M. in Modeling the Hydrogen Bond; Smith, D. A.; American Chemical Society, Washington, DC, 1994; pp 113. Please let me know if I can be of further assistance Regards, Andy Holder -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- UUUU UUU MMM MMKK KKKK CCCC | ANDREW J. HOLDER UU U MM MMK K CC CC | Assoc. Prof. of Comp./Org. Chemistry UU U MMM M MK KK CCC | Dept. of Chemistry UU U M MM MK KK CC CC | University of Missouri-Kansas City UUUUU MMM M MMKK KK CCCC | Kansas City, MO 64110 KK | aholder@cctr.umkc.edu K | (816) 235-2293, FAX (816) 235-5502 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Netters, A few weeks ago, Jeffrey Nauss asked about a comparison between the AM1 and PM3 semiempirical methods. Both of these semiempirical methods are included in most programs that support semiempirical calculations (AMPAC, MOPAC, etc.). Please note that the following discussion is MY OPINION and a compendium of MY EXPERIENCES. I hope you find it somewhat useful. The lead references to each method follows: AM1: Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. J. Am. Chem. Soc. 1985, 107, 3902. PM3: Stewart, J. J. P. J. Comput. Chem. 1989, 10, 209. AM1 stands for "Austin Model 1" and PM3 stands for "Parameterization Method 3". Both methods implement the same basic NDDO theory pioneered by Michael Dewar while at the University of Texas at Austin. The differ- erence is in how the parameters that the semiempirical methods utilize to replace portions of the full ab initio implementation of Hartree-Fock theory. Perhaps the most important difference between AM1 and PM3 is the involvement of the researcher in the parameterization process. PM3 was developed using a largely undirected mathematical optimization process with greatly reduced guidance from chemical knowledge or intuition, an addition that the Dewar methods consider essential. The human researcher knows for which molecules it is necessary to obtain the best fit. For instance, it is useless to obtain parameters for carbon and hydrogen that describe the properties of cubane correctly if the results for benzene are significantly different from experiment. An attentive and knowledgeable chemist can also guide the search into areas of the parameter hypersurface that make sense as far as the absolute magnitude of the parameters themselves are concerned. As with many chemical properties, the parameter values should vary periodically. While this should not unduly constrain the final values, parameters should follow well-defined general trends for proper interaction with other elements. In terms of the actual NDDO model, the actual parameters allowed to vary in the two methods are quite different. In AM1, a large number of values we used from spectroscopy for some of the one-center terms and the other parameters derived with these values fixed. (This is possible only for the lighter elements in the Main Group.) PM3 allowed ALL of these values to float, resulting in substantially more parameters. AM1 also had a quite different concept as to the application of the Guassian functions introduced with AM1 to adjust the core-electron/core- electron repulsion function. Workers in the Dewar group and subsequently in my group see Gaussian functions as PATCHES to the theory, not integral parts. All models fail at some point and the Gaussians were introduced to help with some of the systematic errors in MNDO. Traditionally, these patches were applied to adjust for difficult molecular systems AFTER semiempirical parameters were stabilized. PM3 includes these Gaussian functions (two for each element) FROM THE BEGINNING. Our experience indicates that in such a situtaion, the chemistry os the element will very likely be very strongly effected by the presence of these functions and the importance of the "real", "chemical" parameters will be reduced and swallowed up bu the Gaussians. In short, Gaussians should only be used where absolutely needed, and then viewed with askance. The essence of the difference between the two philosophies is evident: the theoretical basis for the method is either accepted or denied. Significant approximations are made to gain the speed advantage that semiempirical methods enjoy over their ab initio quantum mechanical brethren. But both the ab initio and semiempirical models are based on the Hartree-Fock set of ideas. These ideas possess theoretical rigor as regards solution of the Schrodinger Equation. If one simply views the semiempirical parameters as adjustables within a curve-fit scheme rather than as components of a theoretical model, little faith or importance resides in the meaning of their final values. Simply put, the method of parameterization described above and used so successfully with AM1 and MNDO (and now SAM1) expresses confidence in the theory. With a firmer footing in chemical reality, AM1 parameters are more likely to yield useful results for situations not specifically included in the molecular basis set for parameterization (MBSP). Some Practical Considerations ----------------------------- The differences in errors between the two methods as published are minimal, but that does not relate the real story of how the methods perform differently. Some key points: - PM3 is clearly better for NO2 compounds as a larger number of these were included in the MBSP. - PM3 is usually a little better for geometries, as these were also heavily weighted. - The molecular orbital picture with PM3 is usually different from that expected or that predicted by other methods. This is a direct consequence of the lack of attention paid to the absolute values of Uss and Upp. It can be seen in the lack of performance in ionization potentials. - PM3 charges are usually unreliable, again a result of the rather strange values that some of the parameters take on, even when other experimental data such as heats of formation and geometries are acceptable. This makes PM3 essentially useless for the derivation of molecular m echanics force fields. Perhaps the best known example of this is the case of formamide. The partial charges for the atoms in the molecules are listed below. The lack of any appreciable charge on N has led to a reversal of the actual bond dipole between C and N in this molecule! Atom AM1 PM3 HF/6-31G* --------------------------------------------- O -0.3706 -0.3692 -0.5541 C 0.2575 0.2141 0.5079 N -0.4483 -0.0311 -0.8835 O // H-C \ NH2 - Several papers have been published describing the performance of AM1 vs. PM3: Dewar, M. J. S.; Healy, E. F.; Yuan, Y.-C.; Holder, A. J. J. Comput. Chem. 1990, 11, 541. Smith, D.A. J. Fluor. Chem. 1990, 50, 427 Smith, D.A.; Ulmer, C.W.; Gilbert, M.J. J. Comput. Chem. 1992, 13, 640. - Most reserachers in my experience have stopped using PM3 and have returned to AM1. An Example of Parameterization Values for Aluminum -------------------------------------------------- Parameter AM1 MNDO PM3 Uss, eV -24.353585 -23.807097 -24.845404 Upp, eV -18.363645 -17.519878 -22.264159 zetas, au 1.516593 1.70288 } 1.444161 zetap, au 1.306347 1.073269 betas, eV -3.866822 -0.594301 } -2.670284 betap, eV -2.317146 -0.956550 alpha 1.976586 1.868839 1.521073 Gaussians: Intensity #1, eV 0.090000 - -0.473090 Width #1 12.392443 - 1.915825 Position #1 2.050394 - 1.451728 Intensity #2, eV - - -0.154051 Width #2 - - 6.005086 Position #2 - - 2.51997 The point on the potential surface located by PM3 is significantly different than that located by AM1. This is immediately apparent from the large discrepancy between the Upp values. These are the important one- electron energy values and they have strong influence on the parameter hypersurface. Also, the difference between Uss and Upp for both MNDO and AM1 is about 6 eV. This has been reduced to 2.5 eV in PM3. The real difficulty, however, is in the Beta values. These parameters are the two-center/one- electron resonance terms and are responsible for bonding interactions between atoms. The PM3 values are almost zero, resulting in the conclusion that there is very little bonding between atoms involving aluminum! (Note that the AM1 values for betas and betap spread out around the single MNDO value for beta. This suggests that the MNDO values were reasonable and AM1 adds greater flexibility.) PM3 regains the bonding interactions lost in the low beta values with two strongly attractive Gaussians spanning the bonding region. ******************************************************************************* We did a short note on rotational barriers in branched alkenes: L. A. Burke et al. J. Physical Organic Chem vol 5,614-616(1992). We were surprised at the time that no one else seemed to have published such results. Luke Anthony Burke tel:609-225-6158 Department of Chemistry fax:609-225-6506 Rutgers University e-mail: Camden, NJ 08102 burke@camden.rutgers.edu USA ****************************************************************************** The comparison of AM1 against PM3 has been quite recently discussed on this list. You may try to search trough archives. My three pens to that discuss may be that AM1 absolutely incorrectly describes interaction in small water clusters; while it was known that it gives not correct hydrogen bond geometry for dimers - I found that it also fails for geometry of larger systems: tetramers, octamers etc. The geometry is absolutely different from what we expect for such clusters (as known from ab-initio and MD studies). In the same time PM3 reproduces these geometries acceptably good - difference in oxygen position between PM3 and HF/6-31G* is ~ 0.1 A for octamers. This is a reason that I am now using PM3 in my Molecular Dynamics studies that use semi-empirical energy surface to derive forces (kind of "quantum" dynamics). Mirek --------------------------------------------------------------- dr Miroslaw Sopek MAKO-LAB Computer Graphics Laboratory ul. Piotrkowska 102a 90-026 LODZ, POLAND tel. (48)(42)332946,322346 fax. (48)(42)332937 e-mail: mako@pdi.lodz.pl, sopekmir@mitr.p.lodz.pl --------------------------------------------------------------- ******************************************************************************* 1995 Oct 28 Recently the NET was asked for refs to (1) AM1 compared to PM3, and (2) Sigma-aromaticity. Here are some refs: AM1 cf. PM3 1) Extensive comparison: J Computer-Aided Molecular Design, 4 (1990) Issue 1 (Special issue) ; discusses PM3, AM1 and MNDO 2) W. Thiel, Tetrahedron, 44 (1988) 7393 3) J. J. P. Stewart, J Comp Chem 11 (1990) 543 10 (1989) 209 10 (1989) 221 12 (1991) 320 4) Dewar et al J Comp Chem 11 (1990) 541 5) Smith et al J Comp Chem 13 (1992) 640 6) In a letter to the Net (1995), Andy Holder (SemiChem) said: PM3 is better than AM1 for NO2 compounds and usually a little better for geom's. It is not as good for MO's and is unreliable for charges. Sigma-aromaticity 1) M. J. S. Dewar "Chemical Implications of Sigma Conjugation" J Am Chem Soc 106 (1984) 669 2) Inagaki et al JACS 116 (1994) 5954 3) Ichikawa et al J Phys Chem 99 (1995) 2307 4) Hiberty et al JACS 117 (1995) 7760 =========== Errol Lewars Chem Dept Trent U, Peterborough Ontario Canada ===== *****************************************************************************8 Piotr- We have a paper in press with Spectrochimica Acta comparing AM1 and PM3 for the prediction of carboxylate stretches. Briefly, PM3 is much closer in absolute terms, but AM1 represents differences between compounds more reliably. This is a very limited specific application, of course, and probably only useful to spectroscopists. I would be interested in hearing what others have to say about more general comparisons. Regards, Steve Cabaniss ****************************************************************************** If you mean comparison of conformational energies you might want to have a look at our paper in J.Comp:Chem. 12, 200 (1991). Kind Regards * Klaus Gundertofte * Head, Department of Computational Chemistry * H.Lundbeck A/S * Ottiliavej 9 * DK-2500 Valby - Denmark Fax +45 3630 1385 * Phone +45 3644 2425-3206 * E-mail kgu@lundbeck.dk *************************************************************************** Hi Piotr, The performance of this methods in relation to which property ? If you are interested in heats of formation both are OK with about the same results. For minimum energy conformations PM3 has lots of problems. I performed many calculations with PM3, AM1 and ab initio and PM3 is qualitatively wrong in most cases. For electronic properties I didn't tried PM3. Best regards, Edgardo Garcia Cristol Chem & Biochem University of Colorado BOULDER CO USA **************************************************************************** Note: %0 Journal Article %A Gano, J.E. %A Jacob, E.J. %A Roesner, R. %D 1991 %T Evaluation of PM3, AM1, and MNDO for Calculation of Higher Energy Ionization Potentials %B J. Computat. Chem. %V 12 %P 127-134 James E. Gano, Director Instrumentation Center in Arts and Sciences University of Toledo Toledo, Ohio 43606 Instrumentation Center : http://www.icenter.utoledo.edu Department of Chemistry: http://www.chem.utoledo.edu 419-530-7847 419-530-4033 (FAX) ****************************** THE END ********************************* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Piotr Seliger PPP I TTT SSS EEE L Department of General P P I T S E L and Inorganic Chemistry, PPP I T SSS EE L University of Lodz, P I T S E L Narutowicza 68, P I T SSS EEE LLL 90-136 Lodz, POLAND "The right to knowledge is like E-mail: pitsel@chemul.uni.lodz.pl the right to life" (G.B.Shaw) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-chemistry@ccl.net Thu Nov 2 06:46:47 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id GAA29051; Thu, 2 Nov 1995 06:46:22 -0500 Received: from earn.cvut.cz for strajbl@silicon.karlov.mff.cuni.cz by bedrock.ccl.net (8.7.1/950822.1) id GAA09954; Thu, 2 Nov 1995 06:46:08 -0500 (EST) Received: from ns.karlov.mff.cuni.cz by earn.cvut.cz (IBM VM SMTP V2R1) with TCP; Thu, 02 Nov 95 12:46:44 MET Received: from silicon.karlov.mff.cuni.cz by ns.karlov.mff.cuni.cz id aa13437; 2 Nov 95 11:42 MEZ Received: by silicon.karlov.mff.cuni.cz (931110.SGI/930416.SGI) for @NS.KARLOV.MFF.CUNI.CZ:CHEMISTRY@ccl.net id AA17766; Thu, 2 Nov 95 12:41:38 -0800 Date: Thu, 2 Nov 95 12:41:38 -0800 From: Marek Strajbl Message-Id: <9511022041.AA17766@silicon.karlov.mff.cuni.cz> To: CHEMISTRY@ccl.net Subject: turbomole and g9x Dear CCLers, I am looking for comparison of efficiency of Turbomole and Gaussian9x programs. I appreciate any benchmarks and tests on diferrent platforms for different systems and different types of calculcations. I'll summarize responses. Regards Marek ---------------------------------- Marek Strajbl Insitute of Physics, Ke Karlovu 5, 121 16, Prague, CZ e-mail: From p.mencarelli@caspur.it Thu Nov 2 07:31:49 1995 Received: from axcasp.caspur.it for p.mencarelli@caspur.it by www.ccl.net (8.6.10/950822.1) id HAA29644; Thu, 2 Nov 1995 07:20:34 -0500 Date: Thu, 2 Nov 1995 07:20:34 -0500 Message-Id: <199511021220.HAA29644@www.ccl.net> Received: from aldebaran.sci.uniroma1.it by axcasp.caspur.it with SMTP; Thu, 2 Nov 1995 13:18:44 GMT X-Sender: mencarel@axcasp.caspur.it X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: "Dr. Paolo Mencarelli" Subject: Force Field for C-H - - - PI interactions Hi all, I am an organic chemist interested in carrying out molecular mechanics calculations on complexes formed by cyclophanes, containing aromatic rings, and alkyl ammonium ions. An important component of the interaction energy in the complex should be the C-H - - - PI interactions between the hydrogen of the alkyl groups and the Pi electrons of the aromatic units of the host. All the Force Fields that I know (MM2, MM3, AMBER, MM+,CHARMM) do not have an explicit term for taking into account the above-mentioned interactions. Does anyone know of a force field capable of explicitly handling such interactions? Thanks. Paolo Mencarelli ============================================= Dr. Paolo Mencarelli Dipartimento di Chimica Universita' La Sapienza P.le Aldo Moro, 2 00185 Roma - ITALY tel 06-49913697 fax 06-490631 E-Mail p.mencarelli@caspur.it E-Mail mencarel@xantia.caspur.it ============================================= From kdr3@leicester.ac.uk Thu Nov 2 09:46:50 1995 Received: from vulcan for kdr3@leicester.ac.uk by www.ccl.net (8.6.10/950822.1) id JAA02587; Thu, 2 Nov 1995 09:39:49 -0500 Received: from hawk.le.ac.uk by vulcan with SMTP (PP); Thu, 2 Nov 1995 14:36:14 +0000 From: "Dr K.D. Roth" Message-Id: <5969.199511021436@hawk.le.ac.uk> Subject: PSI88 and transition metals To: chemistry@www.ccl.net (ccl) Date: Thu, 2 Nov 1995 14:36:08 +0000 (GMT) X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 1274 Dear CCL'ers, I am looking for way to display (and plot) molecular orbitals from Gaussian94 calculations. Now, I'm aware of PSI88, but to my knowledge it is a) restricted to atoms up to Ar and b) to a few standard basis sets coming with G94. I'm trying to do calculations on first and second row transition metal complexes, and I am using non-standard basis sets like those of Ahlrichs. Since I am cer- tainly not the first fool (?) doing this, I was wondering, if some kind soul out there has already done the necessary work and has extended PSI88 to con- tain transition metals (I'm almost completely illiterate in FORTRAN, so I can't do it myself ... at least not in a reasonable time :-) ). Any help will be greatly appreciated, in case that there is sufficient interest I'll summarize for the list. Many thanks in advance to all those who will respond. Klaus-Dieter Roth ******************************************************************************** + Dr. Klaus-Dieter Roth + I'm trying hard to prove Department of Chemistry + Murphy's law .... University of Leicester + Leicester LE1 7RH + ... but something always e-mail: kdr3@le.ac.uk + goes wrong ... + ******************************************************************************** From jstewart@fujitsuI.fujitsu.com Thu Nov 2 12:16:52 1995 Received: from mail.barrnet.net for jstewart@fujitsuI.fujitsu.com by www.ccl.net (8.6.10/950822.1) id MAA05876; Thu, 2 Nov 1995 12:12:41 -0500 Received: from fujitsu1.fujitsu.com (fujitsu1.fujitsu.com [133.164.254.1]) by mail.barrnet.net (8.7.1/MAIL-RELAY-LEN) with SMTP id JAA09674 for ; Thu, 2 Nov 1995 09:12:18 -0800 (PST) Received: by fujitsu1.fujitsu.com (4.1/SMI-4.1) id AA06723; Thu, 2 Nov 95 09:13:52 PST Date: Thu, 2 Nov 95 09:13:52 PST From: jstewart@fujitsu.com (Dr. James Stewart) Message-Id: <9511021713.AA06723@fujitsu1.fujitsu.com> To: CHEMISTRY@www.ccl.net Subject: Bug in MOPAC 93 BUG IN MOPAC 93 The calculation of excited state transition moments in MOPAC 93 is faulty, and results of such calculations should not be used. The fault can be demonstrated by running the following job: 1scf meci C.I.=2 H 0.00000000 0 0.0000000 0 0.0000000 0 0 0 0 C 1.11816865 1 0.0000000 0 0.0000000 0 1 0 0 F 1.33613605 1 109.9107649 1 0.0000000 0 2 1 0 Br 1.90383829 1 104.7029401 1 119.6790291 1 2 1 3 I 2.05736002 1 107.2678854 1 -126.1994989 1 2 1 3 This will give the polarization of the transitions as shown below. Transition moments are calculated from state functions using integrals of the type and these MUST be zero if i=j. The output indicates that the `transition' from State 1 to State 1 has a non-zero polarizability. Therefore the calculation is faulty. This bug affects MOPAC 93 only, and appears to be confined to the polarization part of the electronic excited state calculation. James J. P. Stewart STATE ENERGY (EV) Q.N. SPIN SYMMETRY POLARIZATION ABSOLUTE RELATIVE X Y Z 1 -0.011305 0.000000 1 SINGLET A 0.0003 0.0006 0.0019 2 2.755365 2.766670 2 TRIPLET A 3 3.388682 3.399987 3 SINGLET A 0.0542 0.1115 0.3755 4 9.202507 9.213812 4 SINGLET A 0.0025 0.0051 0.0172 From te_meehan@ccmail.pnl.gov Thu Nov 2 14:46:54 1995 Received: from pnl.gov for te_meehan@ccmail.pnl.gov by www.ccl.net (8.6.10/950822.1) id OAA08624; Thu, 2 Nov 1995 14:40:37 -0500 From: Received: from ccmail.pnl.gov by pnl.gov (PMDF V4.3-13 #6012) id <01HX6045XMDC8WVYK4@pnl.gov>; Thu, 02 Nov 1995 11:40:31 -0800 (PST) Date: Thu, 02 Nov 1995 11:37 -0800 (PST) Subject: IRC in MOPAC summary To: chemistry@www.ccl.net Message-id: <01HX6048UCKU8WVYK4@pnl.gov> MIME-version: 1.0 Content-transfer-encoding: 7BIT Zu der Liste, A number of people answered to my inquiry concerning IRC in MOPAC- some nice, some hostile. I will only summarize with Jeff Gosper's input, who covers what everyone said as well as introduces an animation program for the PES. Ummmmm. enticing. However, I must add that I did try this option before I made the inquiry only to get a message that the gradient is too large. I was hoping the Gods of Quantum would impart divine wisdom. Refinement of the transition state obviously is necessary, but subsequent refinements have given me transition states that are ridiculous. I stress ridiculous. Any further comments along these lines would also be greatly appreciated. Danke Schoen, Tim Meehan te_meehan@pnl.gov -------------------------------------------------- Dear Tim, In response to your question about IRC calculations, using IRC=1 will run the IRC calculation in one direction while IRC=-1 will run it in the opposite direction. PS I have just started looking at IRC calculations in MOPAC myself and have developed a program that allows you to analysis the results (produce graphs of variables and 3D models) and will produce an animation (mpeg of flc) of the output =. The name of the program is Re_View. If you have any interesting reaction profiles I would be interested in receiving them and could provide you with an animation of the results. original query: > > I've been trying to run the IRC option in MOPAC, but the > calculation progresses on only one side of the reaction path. > Does anyone use IRC in MOPAC and how can I get it to follow > both sides of a transition state? Thanks for any replies. > > Tim Meehan > te_meehan@pnl.gov /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://http2.brunel.ac.uk:8080/~castjjg \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From richard@biosym.com Thu Nov 2 16:46:55 1995 Received: from bioc1.biosym.com for richard@biosym.com by www.ccl.net (8.6.10/950822.1) id QAA11141; Thu, 2 Nov 1995 16:34:29 -0500 Received: from biff.biosym.com by bioc1.biosym.com (5.64/0.0) id AA17761; Thu, 2 Nov 95 13:32:26 -0800 Received: from intel5.biosym.com by biff.biosym.com (4.1/SMI-4.1) id AA24222; Thu, 2 Nov 95 13:29:50 PST Received: by intel5.biosym.com with Microsoft Mail id <01BAA927.C279F0A0@intel5.biosym.com>; Thu, 2 Nov 1995 13:33:13 -0800 Message-Id: <01BAA927.C279F0A0@intel5.biosym.com> From: Richard Macdonald To: "'chemistry@www.ccl.net'" Subject: Asilomar conf paper Date: Thu, 2 Nov 1995 13:33:12 -0800 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit I remember reading a write-up of the protein modeling challenge held at Asimomar recently (I think it was in Protein Science). But I can not find it now. Could some kind soul point me to the reference? Thanks, richard From patterson@chem.wisc.edu Thu Nov 2 17:31:58 1995 Received: from chem.wisc.edu for patterson@chem.wisc.edu by www.ccl.net (8.6.10/950822.1) id RAA12303; Thu, 2 Nov 1995 17:30:36 -0500 From: Received: from evp by chem.wisc.edu; Thu, 2 Nov 95 16:30 CST Message-Id: <25110216303364@chem.wisc.edu> Date: Thu, 2 Nov 1995 16:33:38 -0600 Subject: CASSCF Tutorial To: chemistry@www.ccl.net Greetings, I am a reasonably experienced user of standard single reference techniques in ab initio calculations, and would now like to branch out and learn about CAS and MRCI. I am looking for anything that might help me in my efforts to understand the complexities of setting up these jobs, and getting good answers. Any leading references to "tutorial" types of publications, as well as opinions on which packages offer the best implementations are welcome. I will summarize for the list. Thanks in advance. Regards, Eric ======================================================================== From the desk of: Eric Patterson voice: (608) 262-0599 Department of Chemistry FAX: (608) 265-4534 University of Wisconsin - Madison email: patterson@chem.wisc.edu 1101 University Ave. Madison, WI 53706 ======================================================================== From ui22204@sunmail.lrz-muenchen.de Thu Nov 2 18:46:57 1995 Received: from cd1.lrz-muenchen.de for ui22204@sunmail.lrz-muenchen.de by www.ccl.net (8.6.10/950822.1) id SAA13216; Thu, 2 Nov 1995 18:33:23 -0500 Received: from sun2.lrz-muenchen.de by cd1.lrz-muenchen.de; Thu, 2 Nov 95 18:32:31 +0100 Received: by sun2.lrz-muenchen.de (4.1/SMI-4.1) id AA10269; Thu, 2 Nov 95 15:54:26 +0100 Date: Thu, 2 Nov 1995 15:54:26 +0100 (MET) From: Eugene Leitl X-Sender: ui22204@sun2 To: chemistry Subject: PDBLib, a C++ macromolecular class library Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII This is the other OO PDB class library I spoke of. Chang, W., et al. (1994), "Design and Application of PDBLib, a C++ Macromolecular Class Library", Oxford University Press. I haven't checked, but documentation is purported to be available at: http://cuhhca.hhmi.columbia.edu -- Eugene From lijian@scripps.edu Thu Nov 2 20:47:00 1995 Received: from scripps.edu for lijian@scripps.edu by www.ccl.net (8.6.10/950822.1) id UAA15025; Thu, 2 Nov 1995 20:36:58 -0500 Received: from pauli.scripps.edu by scripps.edu (5.61/1.34) id AA13130; Thu, 2 Nov 95 17:36:49 -0800 Received: by pauli.Scripps.EDU (4.1/SMI-4.1/TSRI1.0) id AA15164; Thu, 2 Nov 95 17:28:00 PST Date: Thu, 2 Nov 95 17:28:00 PST From: lijian@scripps.edu (Jian Li) Message-Id: <9511030128.AA15164@pauli.Scripps.EDU> To: CHEMISTRY@www.ccl.net Subject: journal name? Could sombody from Italy plaese tell me what is the full name of the journal Rent. Lincei. Sci. Nat. ? Thanks.