From chemistry-request@server.ccl.net Thu Aug 31 02:15:52 2000 Received: from batch14.uni-muenster.de (BATCH14.UNI-MUENSTER.DE [128.176.188.112]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA32237 for ; Thu, 31 Aug 2000 02:15:51 -0400 Received: from ASTERIX.uni-muenster.de (ASTERIX.UNI-MUENSTER.DE [128.176.188.90]) by batch14.uni-muenster.de (Postfix) with ESMTP id 044A110CF for ; Thu, 31 Aug 2000 08:15:44 +0200 (MES) Received: from localhost (chan@localhost) by ASTERIX.uni-muenster.de (8.9.3/8.9.3) with ESMTP id IAA136980 for ; Thu, 31 Aug 2000 08:15:43 +0200 X-Authentication-Warning: ASTERIX.uni-muenster.de: chan owned process doing -bs Date: Thu, 31 Aug 2000 08:15:43 +0200 (MES) From: Chun Chung Chan To: CHEMISTRY@ccl.net Subject: g98 compilation in Suse 6.4 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I have troubles to compile the Gaussian 98 Rev A.9, in a PC, AMD K6 running Suse 6.4. The compilation stopped at l402.exe. bd0402.o: In function `bd0402_': bd0402.o(.text+0x0): multiple definition of `bd0402_' l402.a(bd0402.o)(.text+0x0): first defined here bd0402.o(.data+0x0): multiple definition of `expon3_' ... Linking: make: *** [l402.exe] Error 1 endif The steps I taken to install the package are: 1. Download the tuned blas library and the corresponding f2c library (find the links in www.gaussian.com) 2. in ~/g98/bsd/i386.make, I set GAULIB = $(GAULIBA) $(BLAS) #GAULIB = util.so RUNF77=/usr/pgi/linux86/bin/pgf77 F2CLIB=/usr/lib/libf2c.a 3. "cd /usr/local/src/g98" "export g98root=/usr/local/src" "./bsd/bldg98 > make.log 2>&1" I would be much grateful if anyone of you could help me solve the problem (I did make a search in the web but got no lucks). Many thanks, Jerry ****************************************************************** * Jerry Chun Chung CHAN chan@uni-muenster.de * * Universitaet Muenster * * Institut fuer Physikalische Chemie fax: 0049-251-83-29159 * * Schlossplatz 4-7 voice: 0049-251-83-29157 * * D-48149 Muenster * * Germany * ****************************************************************** From chemistry-request@server.ccl.net Wed Aug 30 17:24:44 2000 Received: from chala.q1.fcen.uba.ar (chala.q1.fcen.uba.ar [157.92.31.25]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA29667 for ; Wed, 30 Aug 2000 17:19:42 -0400 Received: from localhost (damian@localhost) by chala.q1.fcen.uba.ar (8.9.3/8.9.3) with ESMTP id UAA11714 for ; Wed, 30 Aug 2000 20:46:35 +0200 Date: Wed, 30 Aug 2000 20:46:35 +0200 (MEST) From: =?X-UNKNOWN?Q?Dami=E1n_Scherlis?= To: chemistry@ccl.net Subject: Running in parallel Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello. Thanks to Alexander, Richard, Krzysztof Joseph, Peter, Eugene, David and Geoff for answering about running in parallel. Krzysztof was on the right track: the problem was in the shmmax file. I had to change the value of the shared memory for smp. Thanks again. -- Damian Scherlis Department of Physical Chemistry Faculty of Sciences University of Buenos Aires From chemistry-request@server.ccl.net Wed Aug 30 21:13:28 2000 Received: from hestia.its.deakin.edu.au (root@hestia.its.deakin.edu.au [128.184.136.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA30690 for ; Wed, 30 Aug 2000 21:13:24 -0400 Received: from [128.184.88.107] (128-184-88-107.bcs.deakin.edu.au [128.184.88.107]) by hestia.its.deakin.edu.au (8.11.0/8.10.0) with ESMTP id e7V15FD01795; Thu, 31 Aug 2000 12:05:15 +1100 (EST) Mime-Version: 1.0 X-Sender: lim@128.184.136.2 Message-Id: Date: Thu, 31 Aug 2000 10:12:56 +1000 To: "Kuppens, Tom" , "OSC CCL" , "Power, Trevor D." From: "Kieran F Lim (Lim Pak Kwan)" Subject: CCL: summary: NMR shielding Cc: "Dr. Christoph Steinbeck" , schrecke@t12.lanl.gov (Georg Schreckenbach) Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id VAA30691 Hello At 8:26 AM +0200 30/8/2000, Kuppens, Tom [JanBe Extern] wrote: >I'm starting a project on NMR ab-initio calculations. >Does someone have an idea of a good starting point in the literature ? I asked a very similar question a while back on both references and available software but very rudely did not summarise to the list. (mea culpa.) here are the replies which were received at the time. Kieran --------------------------------------------------------------------- At 12:07 PM +0200 15/5/1998, Dr. Christoph Steinbeck wrote: >As to software, there is the C-13 shift prediction module of ChemWindows >(might be Cherwell Scientific), based on HOSE codes, the HyperNMR module >of Hyperchem, which does something ab-initio, and also a web based >prediction applet, also based on HOSE code. For the latter, I don't have >a reference, because I'm travelling right now, and my notebooks >bookmarks are not updated. If you answer to this mail, I'll send you the >URL as soon as I'm back in my office. At 10:43 AM +0200 19/5/1998, Christoph Steinbeck wrote: >Here is the URL that I mentioned regarding this Web-based prediction >module. They now also seem to have inverted the prediction, now comming >from a C-13-NMR-Spektrum to a structure, based on this algorithm >developed at BASF in Germany. They describe it on their page. But there >is also, what you were looking for. >The URL is: http://www.acdlabs.com/ At 9:31 AM -0600 15/5/1998, Georg Schreckenbach wrote: >the question of calculating NMR chemical shifts has been on the CCL every >now and then, and I would recommend that you search the archives. > >This is a very active research area, and there are numerous reviews. >Methods for non-relativistic calculations of NMR chemical shifts are, by >now , fairly well developed for molecules. You can use GAUSSIAN94, for >instance. Gaussian94 has the GIAO method included which is possibly the >most reliable approach towards the "gauge problem". Currently, they have >Hartree-Fock and various DFT methods including GGAs and hybrids. I think >Gaussian98 will have MP2 also. You will, in general, need a good basis set >(6-31+G* at the very least, it is often a good idea to test basis set >convergence), a good geometry (experimentally or optimized at a suitable >levle of theory), good description of correlation. > >Some reviews: > >1. Tossell JA (ed.) (1993) Nuclear Magnetic Shieldings and Molecular >Structure, NATO ASI C386, Kluwer, Dordrecht, The Netherlands. (this is a >book that summarized the state of the art at the time) >2. Jameson CJ (1980-1997) In: Webb GA (ed.) Specialist Periodic >Reports on NMR, Vol. 8-, Royal Society of Chemistry, London. Appears >annually. >3. Fukui H (1987) Magn Reson Rev 11: 205. >4. Chesnut DB (1989) In: Webb GA (ed.) Annual Reports on NMR >Spectroscopy, Vol. 21, Academic Press, New York, p. 51. >5. Kutzelnigg W Fleischer U Schindler M (1990) In: Diehl PS (ed.) NMR >-- Basic Principles and Progress, Vol. 23, Springer-Verlag, Berlin, p. >165. >6. Cremer D Olsson L Reichel F Kraka E (1993) Israel J Chem 33: 369. >7. Chesnut DB (1994) In: Webb GA (ed.) Annual Reports on NMR >Spectroscopy, Vol. 29, Academic Press, New York, p. 71. >8. Chesnut DB (1996) In: Libkowitz KB, Boyd DB (ed.) Reviews in >Computational Chemistry, Vol. 8, Verlag Chemie, New York, p. 245. >9. Gauss J (1996) Ber Bunsenges Phys Chem 99: 1001. >10. de Dios AC (1996) Prog in NMR Spectr 29: 229. >11. Kaupp M Malkina OL Malkin VG (1998) In: Schleyer PRv (ed.) >Encyclopedia of Computational Chemistry, Wiley, New York, in print. > >I like, particularly, the three reviews by Chesnut. The one by Cremer is >also good to get started by getting an idea as to what is involved. The >annual reports by Jameson are very good but also very technical. >Additionally, we have written an "overview" for Theoretical Chemistry >Accounts" that is out already, according to the Springer website >(http://link.springer.de/link/service/journals/00214/tocs.htm, volume 99/2. >You can download it from there if your library has access). I haven't seen >it in print yet. > >The second major part of NMR spectra, spin-spin coupling constants, is >another matter. It is one or several orders of magnitude more difficult to >calculate accurately as compared to the chemical shift, in my opinion. >There are no public programs for it as of yet, apart from the "deMon" >program of Salahub and Malkin; I don't know whether or not they distribute >it. At 10:00 AM +0100 18/5/1998, Peter Tebbutt wrote: >Our product gNMR is an excellent tool for calculating NMR spectra for any >NMR active nucleus. It is possible to calculate spectra either by direct >input of spectral parameters or by drawing a structure in a chemical >drawing program and importing (or pasting) the file. Once the simulation is >found to be satisfactory you may import experimental files and perform an >iterative calculation to extract accurate values of parameters. The program >can be used to import spectra from most common instruments (Bruker, JEOL, >geSun etc). > >In addition gNMR can be used to perform simulations of exchange reactions. >Plrease take a look at our web site: > >http://www.cherwell.com/ProdHome/gnmrhome.html > >where you can download a free demo. At 8:34 AM +0200 28/5/1998, Jerry C.C. Chan wrote: >Original post: > > > I would like to make a literature search on the 31P chemical > > shielding tensor calculation (DFT, ab inito). Could anyone send me > > pointers to the latest works or reviews? > >****************************************************************** >[1] > >Dear Jerry, > >no specific answers, unfortunately. However, a good starting points should >be the annual reviews by C. Jameson >Jameson CJ (1980-1997) In: Webb GA (ed.) Specialist Periodic Reports on >NMR, Vol. 8-, Royal Society of Chemistry, London. > >Otherwise, we have just written a review on DFT calculations of NMR >chemical shifts. It is out already, according to the Springer website >(http://link.springer.de/link/service/journals/00214/tocs.htm, volume 99/2. >You can download it from there if your library has access). I haven't seen >it in print yet. It does not, however, contain much on 31P NMR. But we do >cite some of your papers ... > >In any case, I would like to see your summary! > >Best regards, Georg > >-- >============================================================== >Dr. Georg Schreckenbach Tel: (USA)-505-667 7605 >Theoretical Chemistry T-12 FAX: (USA)-505-665 3909 >M.S. B268, Los Alamos National E-mail: schrecke@t12.lanl.gov >Laboratory, Los Alamos, New Mexico, 87545, USA >Internet: http://www.t12.lanl.gov/~schrecke/ >============================================================== > >[2] > >Hello Jerry, >I recommend you read the chapter by D. B. Chesnut, in Reviews in Computational >Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, >1996, Vol. 8, pp. 245-297. The Ab Initio Computation of Nuclear Magnetic >Resonance Chemical Shielding. > >Donald B. Boyd, Ph.D. >Research Professor of Chemistry >Co-editor, Reviews in Computational Chemistry >Co-editor, Journal of Molecular Graphics and Modelling >Department of Chemistry >Indiana University-Purdue University at Indianapolis >402 North Blackford Street >Indianapolis, Indiana 46202-3274, U.S.A. >E-mail boyd@chem.iupui.edu >Web http://chem.iupui.edu/rcc/rcc.html > >[3] > >Dear Colleague, > >You can try http://macedonia.nrcps.ariadne-t.gr/chemistry/. > > > Your inquiry > > Subject: CCL:31P chemical shielding calculation. > >Yours, > >F.S. Varveri At 11:10 AM +0100 2/6/1998, Renate Buergin wrote: >For further references see: >A. Fürst, E. Pretsch, Anal. Chim. Acta 229, 17 (1990). >E. Pretsch, A. Fürst, M. Badertscher, R. Bürgin and M. E. Munk, J. Chem. >Inf. Comp. Sci. 32, 291-295 (1992). >R. Bürgin Schaller, E. Pretsch, Anal. Chim. Acta 290, 295 (1994). >R. Bürgin Schaller, C. Arnold and E. Pretsch, Anal. Chim. Acta 312, 95-105 >(1995). >R. Bürgin Schaller, M. E. Munk and E. Pretsch, J. Chem. Inf. Comput. Sci. >36, 239-243 (1996). At 8:29 PM -0500 22/1/1999, Miguel Lores Moreira wrote: > >On Thu, 21 Jan 1999, Alessandra Villa wrote: > > > >> > >> I thank you all the persons that answer me and try to help me > >> I summary the answers (4) , maybe it could be halpfull some someone else. > >> Best Regards > >> Alessandra > > > > > > Sorry for jumping in at such a late stage, but I would recommand > >an excellent review on NMR chemical shift as well as spin-spin coupling > >calculations: Chem. Rev. 99, 293-352 (1999). Just from the length, you may > >imagine that the paper should cover extensive areas. Just one quote from > >the review (for fun:-) "We believe that none of the published reviews are > >similar in approach and scope to ours: most concentrate on the results; > >those that discuss the theory, do not have the character of a general > >review" At 2:43 PM -0400 30/7/1999, E. Lewars wrote: >1999 July 30 > >Hello, I can't remember if I sent this summary to the comp chem nerwork >already; anyway, there is a new reply that just came (#6). > Thanks > > E. Lewars >======================= > >1999 July 26 > > REPLIES TO QUESTION ABOUT MP2- cf. HF-LEVEL NMR CHEMICAL SHIFTS > >THE QUESTION: > > > Hello, I read somewhere that NMR chemical shifts calc at the MP2 level are > > somewhat better than at the HF level. Has anyone a reference to this? > > Thanks. > > Thanks very much to all who responded. As you see, I got a lot of >information. > >For people who wish to look at just a few of the refs, I might suggest: >J. Gauss. JCP 99 3629 (1993) >Cheesman et al JCP 104 5497 (1996) >(I haven't yet got hold of the J. Gauss paper in Ber. Bunsenges. Phys. Chem.) >The Chem Rev 1999 review is physical-theoretical rather than a presentation >and analysis of calculated chemical shifts. > >I did a few calcs on B3LYP/6-31G* geometries, using the G94 default >algorithm and the HF/6-31G* and HF/6-311+G(2d,p) wavefunctions. There was >not that much difference between the two basis sets, although the latter took >a lot longer. I was astonished at how accurate the chemical shifts were. > >------------- >THE ANSWERS (#1--#6): > >1999 July MP2 cf. HF NMR SHIFTS > > >#1 >Matthias Hofmann > > > Hello, I read somewhere that NMR chemical shifts calc at the MP2 level are > > somewhat better than at the HF level. Has anyone a reference to this? > > Thanks. > >One early example is: >Decisive Electron Correlation Effects on Computed 11B und 13C NMR Chemical >Shifts. Application of the GIAO-MP2 Method to Boranes and Carbaboranes. >M. Bue\237hl, J. Gauss, M. Hofmann, P. v. R. Schleyer, J. Am. Chem. >Soc., 1993, >115, 12385-12390. > >For other nuclei you might search for early papers by J. Gauss, who first >implemented the GIAO-MP2 methods (and higher correlated methods) in ACES2. > >Regards, >Matthias > -------------------------------------------------------------------- > Dr. Matthias Hofmann | phone: 706 542-7748 > Ctr. for Comp. Quantum Chem. | fax: 706 542-0406 > University of Georgia | e-mail: hofmann2@zopyros.ccqc.uga.edu > Athens, GA 30602-2525 | http://zopyros.ccqc.uga.edu >============----------------------------------------------------------- > > >#2 >Michael D. Bartberger >Jul 21 '99 at 10:42 pm > >Hello: > >You might check the references of J. Gauss; he, along with John >Stanton have published a number of papers (I include references below) on >the computation of checmical shifts with MBPT. Also R.J. Bartlett and >coworkers have investigated shifts and coupling constants at the >CC level. A lot of this is nicely summarized in a recent Chem. Rev. >article by Helgaker et al., 1999, v. 99, 293-352. > >Other possibly useful references follow. > >Best regards, >-Mike Bartberger >UCLA > >+-----------------------------------------------------------------+ >| Michael D. Bartberger, Ph.D. | >| NIH Postdoctoral Fellow TEL: 310.206.0553 | >| Department of Chemistry and Biochemistry FAX: 310.206.1843 | >| University of California, Los Angeles | >| Los Angeles, California 90095-1569 mdb@chem.ucla.edu | >+-----------------------------------------------------------------+ > > Kollwitz, M; Haser, M; Gauss, J. > Non-Abelian point group symmetry in direct second-order many-body > perturbation theory calculations of NMR chemical shifts. > JOURNAL OF CHEMICAL PHYSICS, 1998 MAY 22, V108 N20:8295-8301. > > Gauss, J; Stanton, JF. > Electron correlation effects on the calculated C-13 NMR spectra of vinyl > cations. > THEOCHEM-JOURNAL OF MOLECULAR STRUCTURE, 1997 JUN 30, V398:73-80. > > STANTON JF; GAUSS J; SIEHL HU. > CCSD(T) CALCULATION OF NMR CHEMICAL SHIFTS - CONSISTENCY OF CALCULATED > AND MEASURED C-13 CHEMICAL SHIFTS IN THE > 1-CYCLOPROPYLCYCLOPROPYLIDENEMETHYL CATION. > CHEMICAL PHYSICS LETTERS, 1996 NOV 15, V262 N3-4:183-186. > > KOLLWITZ M; GAUSS J. > A DIRECT IMPLEMENTATION OF THE GIAO-MBPT(2) METHOD FOR CALCULATING NMR > CHEMICAL SHIFTS - APPLICATION TO THE NAPHTHALENIUM AND ANTHRACENIUM IONS. > CHEMICAL PHYSICS LETTERS, 1996 OCT 4, V260 N5-6:639-646. > > GAUSS J. > ACCURATE CALCULATION OF NMR CHEMICAL SHIFTS. > BERICHTE DER BUNSEN-GESELLSCHAFT-PHYSICAL CHEMISTRY CHEMICAL PHYSICS, > 1995 AUG, V99 N8:1001-1008. > > BUHL M; GAUSS J; STANTON JF. > ACCURATE COMPUTATIONS OF SE-77 NMR CHEMICAL SHIFTS WITH THE GIAO-CCSD > METHOD. > CHEMICAL PHYSICS LETTERS, 1995 JUL 21, V241 N3:248-252. > > SIEHL HU; MULLER T; GAUSS J; BUZEK P; and others. > CYCLOPROPYLCYCLOPROPYLIDENEMETHYL CATION - A UNIQUE STABILIZED VINYL > CATION CHARACTERIZED BY NMR SPECTROSCOPY AND QUANTUM CHEMICAL AB INITIO > CALCULATIONS. > JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1994 JUL 13, V116 > N14:6384-6387. > > BUHL M; GAUSS J; HOFMANN M; SCHLEYER PV. > DECISIVE ELECTRON CORRELATION EFFECTS ON COMPUTED B-11 AND C-13 NMR > CHEMICAL SHIFTS - APPLICATION OF THE GIAO-MP2 METHOD TO BORANES AND > CARBABORANES. > JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1993 DEC 29, V115 > N26:12385-12390. > > SCHLEYER PV; GAUSS J; BUHL M; GREATREX R; and others. > EVEN MORE RELIABLE NMR CHEMICAL SHIFT COMPUTATIONS BY THE GIAO-MP2 > METHOD. > JOURNAL OF THE CHEMICAL SOCIETY-CHEMICAL COMMUNICATIONS, 1993 DEC 7, > N23:1766-1768. > > SIEBER S; SCHLEYER PV; GAUSS J. > THE ACCURATE C(2V) PHENONIUM AND BENZENONIUM ION STRUCTURES CONFIRMED BY > CORRELATED GIAO-MP2 NMR CHEMICAL SHIFT CALCULATIONS. > JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1993 JUL 28, V115 > N15:6987-6988. > Pub type: Note. > > GAUSS J; SCHNEIDER U; AHLRICHS R; DOHMEIER C; and others. > AL-27 NMR SPECTROSCOPIC INVESTIGATION OF ALUMINUM(I) COMPOUNDS - ABINITIO > CALCULATIONS AND EXPERIMENT. > JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1993 MAR 24, V115 >N6:2402-2408. > > GAUSS J. > CALCULATION OF NMR CHEMICAL SHIFTS AT 2ND-ORDER MANY-BODY PERTURBATION > THEORY USING GAUGE-INCLUDING ATOMIC ORBITALS. > CHEMICAL PHYSICS LETTERS, 1992 APR 17, V191 N6:614-620. > > PERERA SA; BARTLETT RJ. > STRUCTURE AND NMR SPECTRA OF THE 2-NORBORNYL CARBOCATION - PREDICTION OF > (1)J((CC)-C-13-C-13) FOR THE BRIDGED, PENTACOORDINATE CARBON ATOM. > JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1996 AUG 21, V118 > N33:7849-7850. > > PERERA SA; BARTLETT RJ; SCHLEYER PV. > PREDICTED NMR COUPLING CONSTANTS AND SPECTRA FOR ETHYL CARBOCATION - A > FINGERPRINT FOR NONCLASSICAL HYDROGEN-BRIDGED STRUCTURES. > JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995 AUG 16, V117 > N32:8476-8477. > Pub type: Note. >=============== > > >#3 > MP2 NMR chemical shifts > MONACO@CHEMNA.DICHI.UNINA.IT > Jul 22 '99 at 9:32 am > >Hi >although they were more concerned with MCSCF, the group of Kutzelnigg has >investigated the effect of correlation on the chemical shifts. So you can look >at its bibliography. >As far as I remember, the effects were not amazing. >Of course when the ground state and the first excited ones are very near in >energy, correlation may play a role and paramagnetic contributions become more >difficult to compute. >Good luck >Guglielmo Monaco >Dip. di Chimica >Universit\340 di Napoli >ITALY >============= > >#4 >schrecke@t12mail.lanl.gov > >Hi, > >while I can't find the original references in the moment, I would suggest >to start with some reviews on ab initio NMR calculations: >J. Gauss, Ber. Bunsenges. Phys. Chem. 1995, 99, 1001 >T. Helgaker et al., Chem.Rev.1999, 99, 293 >Both should have something on your question or, at least, give you further >references. Besides, some limited SCF-MP2 comparison is also in B=FChl et al= > >. >J. Phys. Chem. 1995, 99, 4000. > >Best regards, Georg > >P.S. Please summarize to the CCL. > >-------------------- >Dr. Georg Schreckenbach Tel: (USA)-505-667 7605 >Theoretical Chemistry T-12 FAX: (USA)-505-665 3909 >M.S. B268, Los Alamos National E-mail: schrecke@t12.lanl.gov >Laboratory, Los Alamos, New Mexico, 87545, USA >Internet: http://www.t12.lanl.gov/home/schrecke/ ***new location!*** >=================== > > >#5 >Doug Fox >Jul 22 '99 at 12:47 (noon) > > > Errol, > > Check J. Gauss, JCP vol 99 3629 (1993). We draw from this and compare >it with DFT methods in Cheesman et.al. JCP vol 104, 5497 (1996). > > Schleyer has also made comparisons in some of his Boron work but I don't >have a good reference. > > Douglas J. Fox > Director of Technical Support > help@gaussian.com >========================== > > >#6 >Date: Thu, 29 Jul 1999 17:02:04 +0100 (CET) >Subject: Re: CCL:SUMMARY OF NMR SHIFTS, MP2 cf. HF >To: elewars@alchemy.chem.utoronto.ca > >Dear friend, >I would like to call your attention on a recent paper by our group >(Chem.Phys.Lett. 298,113-119, 1998) showing that >the PBE1PBE functional (an hybrid based on the PBE model of Perdew et al.) >provides improved NMR chemical shifts with respect to other >functionals. Note th >at >this is also the case for other propeties (J.Chem.Phys. 110,6158-6170, 1999), >polarizabilities (Chem.Phys.Lett.307,265-271,1999) and UV spectra >(J.Chem.Phys. >number of August 15, 1999 and other papers in press). >Best regards > Enzo > >-------------------------------------------------------------------------- > Vincenzo Barone full professor of Theoretical Chemistry >-------------------------------------------------------------------------- >Dipartimento di Chimica | phone: +39-081-5476503 >Universita' Federico II | fax: +39-081-5527771 >via Mezzocannone 4 | e-mail: enzo@chemna.dichi.unina.it >I-80134 Napoli, Italy | enzo@napo.dichi.unina.it >-------------------------------------------------------------------------- also a recent article by Cheeseman, Predicting Magnetic Properties in ChemNews.Com VOL 10 NO 1 with a full version on the gaussian site http://www.gaussian.com/nmrcomp.htm ------------------------------------------------------------ Dr Kieran F Lim Biol. and Chemical Sciences (Lim Pak Kwan) Deakin University ph: + [61] (3) 5227-2146 Geelong VIC 3217 fax: + [61] (3) 5227-1040 AUSTRALIA mailto:lim@deakin.edu.au http://www.deakin.edu.au/~lim From chemistry-request@server.ccl.net Thu Aug 31 05:47:18 2000 Received: from tibre.ujf-grenoble.fr (tibre.ujf-grenoble.fr [193.54.238.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA00586 for ; Thu, 31 Aug 2000 05:47:14 -0400 Received: from corot.ujf-grenoble.fr (corot.ujf-grenoble.fr [193.54.242.2]) by tibre.ujf-grenoble.fr (Pro-8.9.3/8.9.3/Configured by AD & JE 25/10/1999) with ESMTP id LAA22135 for ; Thu, 31 Aug 2000 11:45:24 +0200 (MET DST) Received: from [193.54.244.187] (poulbot [193.54.244.187]) by corot.ujf-grenoble.fr (AIX4.3/UCB 8.8.8/8.8.5) with ESMTP id LAA26302 for ; Thu, 31 Aug 2000 11:41:26 +0200 Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Sender: tdbruin@chimie Message-Id: Date: Thu, 31 Aug 2000 11:46:23 +0000 To: chemistry@ccl.net From: Theo de Bruin Subject: wavefunction instability vs. spin contamination Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id FAA00587 Dear CCL'ers At the moment we are performing calculations on several (relatively large) di-cobalt complexes using the B3LYP functional and LanL2DZ basis set. Restricted B3LYP calculations yield geometries that fit quite well the corresponding crystal structures. However, from computations with the G98 keyword STABLE it was clear that wavefunctions showed a RHF --> UHF instability. For example: Eigenvector 1: Triplet-?Sym Eigenvalue = -0.0067007 (it seems that the negative eigenvalue is rather small....?) Performing the same calculations with the UNrestricted B3LYP (using guess=mix and changing the DIIS for the QC algorithm) does yield stable wavefunctions, which are about 0.1 to 0.2 kcal/mol lower in energy. However, the obtained geometries with the unrestricted wavefunctions deviate substantially from the crystal structures (delta r(Co-Co) > 0.2 angstrom!), and moreover there is a large spin contamination (S**2 is up to 0.74 for a singlet ground state), which probably results from the (too) large Co-Co distance. We have calculated that the triplet electron configuration has a much higher energy (> 50 kcal/mol). Unfortunately, we were not able to perform successful CASSCF calculations to find out if there was contribution of the triplet in the ground state, since the necessary number of electrons and orbitals in the active space was far too large. Since MP2 calculations on 1st row transition metals are unreliable, higher (than HF or DFT) correlations methods are completely impractical for this size of systems, and the instability seems to be very small (small neg. eigenvalue and small energy difference between restr. and unrestr. wavefunctions), it is very tempting to continue the work with the restricted B3LYP method. Especially, because we are mostly interested in the geometries and their relative energies. Does anybody have some tips or advice how to continue? Best regards, Theo de Bruin ----------------------------------------------------------------------- Theodorus J.M. de Bruin Phone +33 4 76 63 56 28 Université Joseph Fourier Fax +33 4 76 51 43 82 LEDSS VII Chimie Théorique E-mail theo.de-bruin@ujf-grenoble.fr UMR CNRS 5616 Bâtiment 52 - Chimie Recherche DU BP 53 38041 Grenoble Cedex 9 FRANCE ----------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Aug 31 08:29:43 2000 Received: from server.biokemi.su.se (server.biokemi.su.se [130.237.179.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id IAA01974 for ; Thu, 31 Aug 2000 08:29:42 -0400 Received: from mail.biokemi.su.se (unverified [130.237.179.175]) by server.biokemi.su.se (EMWAC SMTPRS 0.83) with SMTP id ; Thu, 31 Aug 2000 14:30:46 +0200 Sender: zhang@ccl.net Message-ID: <39AE4EBC.ABED0BC@mail.biokemi.su.se> Date: Thu, 31 Aug 2000 14:25:32 +0200 From: Xiao-Ping Zhang Reply-To: zhang@biokemi.su.se X-Mailer: Mozilla 4.72 [en] (X11; U; Linux 2.2.14-12 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Summary for Autodock3 - help for peptide docking Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, This is the summary for my question concerning autodock 3 posted to the ccl net on August 22. Thank Csaba, Susanna for your response to my quetion: The original question: > > Does anybody has successful experience in peptide docking > with autodock (I only saw one paper which is in the autodock > reference list)? I tried to dock some peptides to a > macromolecule. Biochemical data showed the binding > difference between different peptides. I hope autodock can > repeat the experimental results. Unfortunately, although > autodock 3 can find the binding site with high accuracy, but > it can not discriminate the peptides for binding in my > test(SA and LGA showed the similar results). Any suggestions > for peptide docking with autodock 3 are highly appreciated. > Here is the answer from Susanna: > Hi Xiao-Ping, > > I have noticed in my work that even if autodock very well finds the right > binding modes for ligands, the results don't correlate to experimental results. > I was trying to use autodock 3 to dock small ligands that showed different > biological activitites and tried to find out structure-activity data. > Unfortunately autodock seemed to give good results for bad ligands as well. > Maybe it was our biological data that was inaccurate, but my experience was that > the program couldn't discriminate between different ligands, it was only good > for finding out the best binding modes. The user has to find out the reasons why > some ligands are better than other visually , not by comparing calculated > energies. > > I hope this was useful information. > > Best regards, Susanna > > ************************** > Susanna Alho > Pharmacy student > Helsinki University > Finland > ************************** and here is the answer from Csaba, > Dear Xiao-Ping, > > I am working on docking small peptides to larger ones. You are absolutely > right, there are only a few studies on this special topic, and, therefore > these peptide-peptide dockings are in experimental state, as I can see > this time. > My goal is the same as yours: I would like to explain experimental results > via docking, and first of all I need results, which are not the opposite > of the experimental ones. > In my first studies /it will be submitted in a week for publication/ I > used the in vacuo 2.4 version of AutoDock and MC/SA, of course. Now I am > working on an AIDS-related topic. > In MC/SA calculations the main question/for me/ is the initial RT value > for annealing. What value do you think is good for 5-6 peptides. As a > first > try in my last work I used the default 616, but I had many misdocked > strustures, which had small intermol. int. act. energies. I set the > acc./rejs. to 10000 or more and let all the torsions free, except of the > amide bonds. > In GA I used larger number of minimum serach steps too. > The new version /3.0.5/ gave smaller energy /Gibbs function/ values, > compared to the earlier, which is no wonder, but first time made me > thinking. > That is all for now. > Please, write me, what problems occured in your practice and if you found > a solution for them, or not. > Regards, > Csaba. > _______________________________________ > Csaba Hetenyi, M.Sc., Ph.D. student > University of Szeged > Dept. of Medical Chemistry > Addr.:H-6720 Szeged, Dom ter 8, Hungary ****************************** Xiao-Ping Zhang Department of Biochemistry Arrhenius Laboratories of Natural Sciences Stockholm Universities 106 91 Stockholm Sweden Phone: 046-08-162472 /162582 Fax: 046-08-153679 e-mail: zhang@biokemi.su.se From chemistry-request@server.ccl.net Thu Aug 31 10:25:52 2000 Received: from smtpsrv0.isis.unc.edu (smtpsrv0.isis.unc.edu [152.2.1.139]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA02874 for ; Thu, 31 Aug 2000 10:25:52 -0400 Received: from unc.edu (calcite.oit.unc.edu [152.2.22.162]) by smtpsrv0.isis.unc.edu (8.9.3/8.9.1) with ESMTP id KAA14135 for ; Thu, 31 Aug 2000 10:25:39 -0400 (EDT) Sender: cdpoon@smtpsrv0.isis.unc.edu Message-ID: <39AE6AE3.51553E86@unc.edu> Date: Thu, 31 Aug 2000 10:25:39 -0400 From: "C. D. Poon" Organization: University of North Carolina X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Running Spartan under LSF Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I have a couple of questions concerning running Spartan under Load Sharing Facility (LSF). Hopefully, some of you have experience with it and give me a hand. When I invoke Spartan under LSF, Spartan starts but it creates another process with new ppid. So, LSF thinks that the Spartan job is done but in fact, Spartan just gets started. I wonder whether anyone has a work around for that. Since Spartan drops outside of LSF in no time, needless to say, all jobs submitted under Spartan GUI will be run outside LSF queue. Here is my work around. Once a Spartan job is created, it actually creates a new directory with all input, output files in it. Instead of selecting "Submit" in the GUI, the work around is to locate that directory in an UNIX terminal, use the LSF command to invoke "spartan -x directory_name". Is there a way to modify the "Submit" in the GUI to invoke LSF command? Thank you very much. C. D. Poon University of North Carolina at Chapel Hill. From chemistry-request@server.ccl.net Thu Aug 31 13:55:19 2000 Received: from research.neu.edu (research.neu.edu [129.10.1.80]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA03809 for ; Thu, 31 Aug 2000 13:55:18 -0400 Received: from localhost (maryjo@localhost) by research.neu.edu with ESMTP id NAA16632 for ; Thu, 31 Aug 2000 13:55:03 -0400 (EDT) X-Authentication-Warning: research.neu.edu: maryjo owned process doing -bs Date: Thu, 31 Aug 2000 13:55:03 -0400 (EDT) From: Maryjo Ondrechen To: chemistry@ccl.net Subject: oxo-bridged dimers of Zn or Co Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello everybody. Please help me. I am searching for references to calculations on mu-oxo-bridged dimers of Zn or Co. Zn-O-Zn or Co-O-Co Thanks very much in advance. Mary j.o. From chemistry-request@server.ccl.net Thu Aug 31 09:20:19 2000 Received: from server.biokemi.su.se (server.biokemi.su.se [130.237.179.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA02549 for ; Thu, 31 Aug 2000 09:20:19 -0400 Received: from mail.biokemi.su.se (unverified [130.237.179.175]) by server.biokemi.su.se (EMWAC SMTPRS 0.83) with SMTP id ; Thu, 31 Aug 2000 15:21:22 +0200 Sender: zhang@ccl.net Message-ID: <39AE5A99.7AF018DA@mail.biokemi.su.se> Date: Thu, 31 Aug 2000 15:16:09 +0200 From: Xiao-Ping Zhang Reply-To: zhang@biokemi.su.se X-Mailer: Mozilla 4.72 [en] (X11; U; Linux 2.2.14-12 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: ligand broken after docking in autodock 3.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi, I have another problems for peptide docking with autodock 3.0. (1) If I define tortions for the peptide ligand, I got a docked peptide which contains a broken backbone (displayed in molecular modeling programs). The distance between the atoms where the bond broken was about 4.0 - 4.5 Å. (2) I always get a docked peptide with many missed atoms. How could we keep a peptide ligand intact during docking? (3) Concerning the flexibility of peptide ligand, we can find the following information in autodock homepage: "Testing the side chain flexibility in AutoDock 4.0 We have now added side chain flexibility to AutoDock, and we are now in the process of testing this." Does that mean that autodock3 can not handle the side chain tortions even if you can define the tortions for side chain with "autotors3"? (4) What is the best program for peptide docking, commercial and free? Thank you advance for your reply. Sincerely, Xiao-Ping Zhang ****************************** Xiao-Ping Zhang Department of Biochemistry Arrhenius Laboratories of Natural Sciences Stockholm Universities 106 91 Stockholm Sweden Phone: 046-08-162472 /162582 Fax: 046-08-153679 e-mail: zhang@biokemi.su.se From chemistry-request@server.ccl.net Thu Aug 31 11:44:45 2000 Received: from nets5.rz.rwth-aachen.de (nets5.rz.RWTH-Aachen.DE [137.226.144.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA03276 for ; Thu, 31 Aug 2000 11:44:44 -0400 Received: from zosia (zosia.dorf.RWTH-Aachen.DE [134.130.59.212]) by nets5.rz.rwth-aachen.de (8.10.1/8.10.1/5) with SMTP id e7VFiUM05864; Thu, 31 Aug 2000 17:44:30 +0200 (MET DST) Message-ID: <001701c01362$c238d0c0$d43b8286@dorf.rwthaachen.de> From: "Krzysztof Radacki" To: "Alexander Hofmann" Cc: References: Subject: Re: CCL:Linux settings to run in parallel Date: Thu, 31 Aug 2000 17:47:24 +0200 Organization: AC RWTH Aachen MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6600 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 Just edit it with vi or whatever editor you like. Only one small problem is that after each restart it has old value. So what I did was adding to some script the line echo "400000000" > /proc/sys/kernel/shmmax (I belive that it was /etc/profile but unfortunately my linux computer is not available for me in next two weeks, so i can't proof it). mfg kris ----- Original Message ----- From: "Alexander Hofmann" To: "Krzysztof Radacki" Sent: Thursday, August 31, 2000 9:08 AM Subject: Re: CCL:Linux settings to run in parallel > Hi Krzys, > > would you please tell me, how to change the shmmax? > > > Thanks > > Alex > > > > > --- > > Dr. Alexander Hofmann > Institut fuer Angewandte Chemie Berlin-Adlershof e.V. > Richard-Willstaetter-Str. 12 > > D-12489 Berlin > > hofmann@aca-berlin.de > > Tel.: 030/6392-4408 > Fax.: 030/6392-4350 > > http://www.aca-berlin.de > > PGP-Private key: > http://www.uni-leipzig.de/~quant/hofmann/alexander.hofmann.pubkey.asc > > From chemistry-request@server.ccl.net Thu Aug 31 14:21:56 2000 Received: from hotmail.com (f209.law9.hotmail.com [64.4.9.209]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA03998 for ; Thu, 31 Aug 2000 14:21:56 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 31 Aug 2000 11:19:57 -0700 Received: from 193.251.53.140 by lw9fd.law9.hotmail.msn.com with HTTP; Thu, 31 Aug 2000 18:19:57 GMT X-Originating-IP: [193.251.53.140] From: "Alexandre Hocquet" To: elewars@trentu.ca Cc: chemistry@ccl.net Subject: Re: CCL:SUMMARY DFT ORBITALS, WF Date: Thu, 31 Aug 2000 18:19:57 GMT Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 31 Aug 2000 18:19:57.0850 (UTC) FILETIME=[119737A0:01C01378] >(2) The Fukui function (R. G. Parr and W. Yang, J Am Chem Soc, 1984, >106, 4049) seems to be always discussed in the context of DFT; yet this >function is "a chemical reactivity index in the sense of the >frontier-electron theory of reactivity..." (R. G. Parr and W. Yang, >"Density-Functional Theory of Atoms and Molecules", Oxford, New York, >1989, p. 101). But in pure DFT theory there are no frontier orbitals. >Isn't this strange? Dear E. Lewars, To add a late 2 francs contribution, a clear distinction between "computational" dft and "conceptual" dft would help. Computational dft is a tool used to compute quantum mechanics of chemical systems that has advantages and shortcomings, like questionnable virtual orbitals, etc... Conceptual dft, whose bible is the book of Parr and Yang, is a genuine theory of molecular electronic structure as described by quantum mechanics. As has been pointed out, the concept of fukui functions may then be defined without explicitely referring to frontier orbitals. Furthermore, concepts defined in conceptual dft may be computed by other tools like a HF calculation. For example, if one approximates the chemical potential as the mean of Elumo and Ehomo, and feels the lumo is poorly described by a Kohn Sham orbital he may resort to HF orbitals. Yours, ------------------------------------------------------------ Alexandre HOCQUET Laboratoire de Physicochimie Biomoléculaire et Cellulaire ESA CNRS 7033 hocquet@lpbc.jussieu.fr Fax: 0144277560 (do not dial first 0 from abroad) LPBC, case courrier 138 4 Place Jussieu, 75252 PARIS Cedex 05 France ------------------------------------------------------------ _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. Share information about yourself, create your own public profile at http://profiles.msn.com. From chemistry-request@server.ccl.net Thu Aug 31 14:57:03 2000 Received: from terra.ifi.unicamp.br (terra.ifi.unicamp.br [143.106.6.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA04519 for ; Thu, 31 Aug 2000 14:56:39 -0400 Received: from ifi.unicamp.br (lua [143.106.6.13]) by terra.ifi.unicamp.br (8.9.3/8.9.3) with ESMTP id PAA05140 for ; Thu, 31 Aug 2000 15:54:35 -0300 (BSC) Received: (from daemon@localhost) by ifi.unicamp.br (8.9.3/8.9.3) id PAA17249 for ; Thu, 31 Aug 2000 15:54:32 -0300 (BSC) Received: from apos17a.ifi.unicamp.br(143.106.39.178) via SMTP by lua.ifi.unicamp.br, id smtpdAAAa004DR; Thu Aug 31 15:54:22 2000 Message-Id: <4.3.2.7.0.20000831154828.00b4ea60@143.106.6.13> X-Sender: dasf@143.106.6.13 X-Mailer: QUALCOMM Windows Eudora Version 4.3.2 Date: Thu, 31 Aug 2000 15:55:11 -0300 To: CHEMISTRY@ccl.net From: Demetrio Antonio da Silva Filho Subject: Conformational Search Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id OAA04545 Dear CCL'ers, I need to make a conformational search to study the interactions between two molecules. I tried Hyperchem 6.0 but I as far as I understood the manual, it isn't possible to accomplish this task because the atoms whose define the dihedral angle should belong to the same molecule. Does anybody knows how I can do it? I have access to Gaussian, Gamess, Hyperchem and Titan. Thanks in advance, Demétrio Filho _____________________________________ Demetrio A. da Silva Filho UNICAMP - IFGW Prédio D - Sala 17 CEP 13083-970 C.Postal 6165 Campinas - SP - Brasil _____________________________________ "Se não houver frutos, valeu a beleza das flores. Se não houver flores, valeu a sombra das folhas. Se não houver folhas, valeu a intenção da semente." Henfil From chemistry-request@server.ccl.net Thu Aug 31 16:12:06 2000 Received: from qtp.ufl.edu (zwart.qtp.ufl.edu [128.227.89.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA05833 for ; Thu, 31 Aug 2000 16:12:05 -0400 Received: from pc1 (pc1 [128.227.192.187]) by qtp.ufl.edu (8.9.1a/8.9.1) with SMTP id QAA05707; Thu, 31 Aug 2000 16:11:34 -0400 (EDT) Message-ID: <00ae01c01388$13659bc0$bbc0e380@qtp.ufl.edu> From: "Stefan Fau" To: "Demetrio Antonio da Silva Filho" Cc: "CCL - all" References: <4.3.2.7.0.20000831154828.00b4ea60@143.106.6.13> Subject: Re: Conformational Search Date: Thu, 31 Aug 2000 16:14:32 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi Demetrio, Gaussian with opt(modredundant) should work. Have a look at http://www.gaussian.com/techinfo.htm for the details. Stefan ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu Quantum Theory Project | (352) 392-6714 University of Florida Gainesville, FL 32611-8435