From val@nmr1.ioc.ac.ru Tue Oct 14 02:30:30 1997 Received: from nmr1.ioc.ac.ru for val@nmr1.ioc.ac.ru by www.ccl.net (8.8.3/950822.1) id BAA06900; Tue, 14 Oct 1997 01:55:44 -0400 (EDT) Received: from nmr-v.ioc.ac.ru (nmr-v.ioc.ac.ru [193.233.3.213]) by nmr1.ioc.ac.ru (8.6.12/8.6.9) with SMTP id JAA06783; Tue, 14 Oct 1997 09:49:23 +0400 Message-ID: <3442FB5F.1B31@nmr1.ioc.ac.ru> Date: Mon, 13 Oct 1997 21:55:59 -0700 From: "Ananikov V.P." Reply-To: val@nmr1.ioc.ac.ru Organization: IOCh X-Mailer: Mozilla 3.0Gold (Win16; I) MIME-Version: 1.0 To: Gustavo de Miranda Seabra CC: chemistry@www.ccl.net Subject: Re: CCL:Help on GAMESS References: <344261A7.CF23F2C8@npd.ufpe.br> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi! Try: $CONTRL SCFTYP=UHF RUNTYP=OPTIMIZE ECP=SBK $END $CONTRL EXETYP=CHECK $END $DATA -- Geometria de equilibrio do ZrF4 TD Zircon 40 0.0 0.0 0.0 SBK Fluor 9 1.24 1.24 1.24 N31 6 $END For some notes about TD symmetry take a look at the page 2-16 in the manual. best wishes, Valentin. Valentin P. Ananikov NMR Laboratory N.D. Zelinsky Institute of Organic Chemistry Leninsky Prospect 47 Moscow 117913 Russia e-mail: val@nmr1.ioc.ac.ru Fax (7095) 1355328 Phone (7095) 1359094, (7095) 9383536 > > Hello all, > > I'm wondering if there is someone who can help me on GAMESS. I'm > trying to > run a test calculation on tetrahedral ZrF4, but when I enter with the > geometry unique > atoms, GAMESS gives me an octahedra! My question is simple: What's > wrong? > The input and the result I have is following below. I thank in advance > any help you > could give-me. > > INPUT: > > $CONTRL SCFTYP=UHF RUNTYP=OPTIMIZE ECP=SBK $END > $CONTRL EXETYP=CHECK $END > $DATA > -- Geometria de equilibrio do ZrF4 > TD > > Zircon 40 0.0 0.0 0.0 > SBK > > Fluor 9 0.0 0.0 2.15 > N31 6 > > $END > > OUTPUT: > INTERNUCLEAR DISTANCES (ANGS.) > ------------------------------ > > ZIRCON FLUOR FLUOR > FLUOR FLUOR FLUOR FLUOR > > 1 ZIRCON 0.0000000 2.1500000 * 2.1500000 * > 2.1500000 * 2.1500000 * 2.1500000 * 2.1500000 * > 2 FLUOR 2.1500000 * 0.0000000 3.0405592 > 3.0405592 3.0405592 3.0405592 4.3000000 > 3 FLUOR 2.1500000 * 3.0405592 0.0000000 > 4.3000000 3.0405592 3.0405592 3.0405592 > 4 FLUOR 2.1500000 * 3.0405592 4.3000000 > 0.0000000 3.0405592 3.0405592 3.0405592 > 5 FLUOR 2.1500000 * 3.0405592 3.0405592 > 3.0405592 0.0000000 4.3000000 3.0405592 > 6 FLUOR 2.1500000 * 3.0405592 3.0405592 > 3.0405592 4.3000000 0.0000000 3.0405592 > 7 FLUOR 2.1500000 * 4.3000000 3.0405592 > 3.0405592 3.0405592 3.0405592 0.0000000 > > * ... LESS THAN 3.000 > > -- > > ----------------------------------------------------------------------------------- > > Gustavo de Miranda Seabra > MSc Student in Chemistry E-Mail: seabra@npd.ufpe.br > Universidade Federal de Pernambuco - Recife - Pernambuco - Brazil > ----------------------------------------------------------------------------------- > From jsl@virgil.ruc.dk Tue Oct 14 06:30:32 1997 Received: from emma.ruc.dk for jsl@virgil.ruc.dk by www.ccl.net (8.8.3/950822.1) id GAA08020; Tue, 14 Oct 1997 06:29:20 -0400 (EDT) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by emma.ruc.dk (8.8.5/8.8.5) with ESMTP id MAA14839; Tue, 14 Oct 1997 12:30:27 +0200 (MET DST) Received: from VIRGIL/MAILQUEUE by virgil.ruc.dk (Mercury 1.21); 14 Oct 97 12:20:27 +0100 Received: from MAILQUEUE by VIRGIL (Mercury 1.21); 14 Oct 97 12:20:18 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "Eugene G. Noda" Date: Tue, 14 Oct 1997 12:20:15 +0100 Subject: Re: CCL:Absorption spectra from ZINDO/S CC: chemistry@www.ccl.net Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <1C1E6730FB3@virgil.ruc.dk> Eugene G. Noda : > In Options Dialog Box (Setup Menu) for ZINDO/S method there > are the Overlap Weighting Factors, which can be manually modified > in the region 0-2. Default values of sigma-sigma parameter is > 1,267 and pi-pi parameter is 0,64. > > So the questions is: > > 1. Whether we can change these parameters to calculate the correct > absorption spectra and how the values of these parameters ought to > be estimated? Dear Eugene: The choice of the pi-pi overlap weighting factor in ZINDO/S is crucial to the results of the model. Unfortunately, HyperChem has chosen to adopt the value 0.64 as the default value. This is very misleading, because in almost all practical applications, one should adopt a value close to 0.585. Krassimir Stavrev thus recently communicated the following details regarding the choice of overlap weighting factor: Stavrev, Krassimir , Mon, 21 Jul 1997: | ..... The value of 0.64 has been successfully used for | triplets spectroscopy, in which case it was shown to yield better | results than the 0.585 factor, see the original work of Zerner and | co-authors quoted in the Computational Chemistry manual, p.295. The | other value, 0.585, is most commonly used in the studies of | transition-metal and organic systems. To my knowledge, the 0.64 value | has not been very well tested and was applied only to triplet-triplet | excitations. In view of this situation, it is not understandable why HyperChem has chosen to adopt 0.64 as the default value, a choice that is likely to lead many users astray! Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/dis/chem/psos/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From seabra@NPD.UFPE.BR Tue Oct 14 07:30:41 1997 Received: from NPD1.NPD.UFPE.BR for seabra@NPD.UFPE.BR by www.ccl.net (8.8.3/950822.1) id GAA08161; Tue, 14 Oct 1997 06:51:21 -0400 (EDT) Received: from danon (danon.dqf.ufpe.br) by NPD.UFPE.BR (PMDF V5.1-4 #20469) with ESMTP id <01IOSFK69MV4001QZE@NPD.UFPE.BR> for chemistry@www.ccl.net; Tue, 14 Oct 1997 07:50:39 GMT-3 Date: Tue, 14 Oct 1997 08:00:53 -0300 From: Gustavo de Miranda Seabra Subject: Thanks on GAMESS To: Computational Chemistry Letters Message-id: <344350E5.5C6807B7@npd.ufpe.br> MIME-version: 1.0 X-Mailer: Mozilla 4.0 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Priority: 3 (Normal) I would like to thank all those answered my question about GAMESS input. As I have recived a great number of replies, I want to thank all of you at once. My question was about how to make the input of an tetrahedral molecule on GAMESS using the simmetry. The answer is that I must define the central atom (in 0,0,0), and one of the corner atoms in the corner of the cube (1,1,1). It cannot be over any of the axis (x, y or z) nor planes (xy, xz, yz). With the answers you sent me, this point was solved and I managed to run the tetrehedral molecule. Thank you very much. Sincerely, -- ----------------------------------------------------------------------------------- Gustavo de Miranda Seabra MSc Student in Chemistry E-Mail: seabra@npd.ufpe.br Universidade Federal de Pernambuco - Recife - Pernambuco - Brazil ----------------------------------------------------------------------------------- From D.A.Tilbrook@mds.qmw.ac.uk Tue Oct 14 09:30:36 1997 Received: from netsrv.lhmc.ac.uk for D.A.Tilbrook@mds.qmw.ac.uk by www.ccl.net (8.8.3/950822.1) id JAA08831; Tue, 14 Oct 1997 09:23:09 -0400 (EDT) Received: from lhmc-fs.mds.qmw.ac.uk (LHMC-FS.lhmc.ac.uk [161.23.16.195]) by netsrv.lhmc.ac.uk (8.6.12/8.6.12) with ESMTP id OAA07302 for ; Tue, 14 Oct 1997 14:24:32 +0100 Received: from LHMC/SMTPMAIL by lhmc-fs.mds.qmw.ac.uk (Mercury 1.21); 14 Oct 97 14:16:05 GMT0BST Received: from SMTPMAIL by LHMC (Mercury 1.21); 14 Oct 97 14:15:43 GMT0BST From: "David A Tilbrook (DMS) 3241" Organization: St. Bart's and the Royal London Med To: chemistry@www.ccl.net Date: Tue, 14 Oct 1997 14:15:39 GMT0BST Subject: Compiling TINKER under GNUwin32 X-Confirm-Reading-To: "David A Tilbrook (DMS) 3241" X-pmrqc: 1 Return-receipt-to: "David A Tilbrook (DMS) 3241" Priority: normal X-mailer: Pegasus Mail/Windows (v1.22) Message-ID: <526D5B24F03@lhmc-fs.mds.qmw.ac.uk> Has anybody out there managed to use GNUwin32 to successfully compile G77 and then to get all the parts of TINKER to compile and run sucessfully. Our group is trying to do this at the moment and are having a lot of problems. We tried compiling the code under the NAG FTN90 compiler and got some rather peculiar results. Does anyone know of a list of known bugs and fixes for the TINKER code? Any help or advice would be very gratefully accepted. Kindest Regards and thanks in advance David Tilbrook ********************************************************** David A. Tilbrook Biomaterials in Relation to Dentistry IRC in Biomedical Materials, B.M.S 2.21.2 Queen Mary and Westfield College (East Gate), Mile End Road, London E1 4NS Tel: 0171 2957974 Fax: 0171 2957979 e-mail D.A.Tilbrook@mds.qmw.ac.uk ********************************************************** From Daniel.Hoffmann@GMD.DE Tue Oct 14 10:30:34 1997 Received: from mail.gmd.de for Daniel.Hoffmann@GMD.DE by www.ccl.net (8.8.3/950822.1) id JAA08902; Tue, 14 Oct 1997 09:32:52 -0400 (EDT) Received: from boyer by mail.gmd.de with SMTP id AA13237 (5.67b8/IDA-1.5 for ); Tue, 14 Oct 1997 15:32:49 +0200 Received: from GMD.DE (localhost) by boyer with SMTP id AA21529 (5.67b/IDA-1.5 for ); Tue, 14 Oct 1997 15:32:48 +0200 Sender: hoffmann@GMD.DE Message-Id: <34437480.D7DF0BC2@GMD.DE> Date: Tue, 14 Oct 1997 15:32:48 +0200 From: Daniel Hoffmann Organization: GMD - German National Research Center for Information Technology X-Mailer: Mozilla 4.03 [en] (X11; I; SunOS 5.6 sun4u) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: Workshop Monte Carlo Approach to Biopolymers and Protein Folding Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Monte Carlo Approach to Biopolymers and Protein Folding 3-5 December 1997 HLRZ, Forschungszentrum Juelich, Germany The HLRZ Supercomputing Center in Juelich has a tradition of organizing an annual international workshop on an important topic to which Computational Physics makes a major contribution. After "Supercomputers in Brain Research" (1994), "Traffic and Granular Flow" (1995), "Friction, Arching, Contact Dynamics" (1996), this year the topic will be "Monte Carlo Approach to Biopolymers and Protein Folding". The main emphasis will be on protein folding. This is widely recognized as one of the main problems in biological physics. But related fields will also be covered, ranging from supercoiling of DNA and simulations of semi-dilute solutions of homopolymers to relaxation in glassy systems. From the technical side, the main emphasis will be on Monte Carlo simulations. Traditionally, the field of protein folding is dominated by Molecular Dynamics simulations. Monte Carlo methods are less constrained in the possible moves, and recent years have seen a steady stream of novel methods which actually exploit this freedom. One purpose of the workshop will be to find out whether progress in Monte Carlo methods will ultimately allow to determine the structure of large proteins from their amino acid sequences. Topics which will be discussed include therefore algorithms for simulating equilibrium and nonequilibrium problems, actual simulations of model and realistic biopolymers, theories of folding pathways, determinations of effective potentials, statistical concepts derived from disordered systems, and data-based approaches to protein folding. Invited speakers are: H.-S. Chan U. Hansmann W. Krauth D. Thirumalai P. Derreumaux D. Hoffmann H. Meirovitch R. Zimmer E. Domany A. Irbaeck H. Orland D. Frenkel M. Karplus A.Z. Panagiotopoulos W.F. van Gunsteren A. Kolinski E. Shakhnovich Participants are invited to present their research at a poster session. Organizers: Peter Grassberger Gerard T. Barkema Walter Nadler For more information see http://w3.hlrz.kfa-juelich.de/HLRZ/Workshops.html On behalf of the organizers Daniel Hoffmann From john@xray.bmc.uu.se Tue Oct 14 11:30:45 1997 Received: from XRAY.BMC.UU.SE for john@xray.bmc.uu.se by www.ccl.net (8.8.3/950822.1) id LAA09460; Tue, 14 Oct 1997 11:04:16 -0400 (EDT) Received: from ronja.bmc.uu.se by XRAY.BMC.UU.SE with SMTP; Tue, 14 Oct 1997 16:57:26 +0200 (MET) Date: Tue, 14 Oct 1997 17:01:32 +0200 (W. Europe Daylight Time) From: John Marelius Reply-To: John Marelius To: ramon kleber da rocha cc: Computational Chemistry Mailing List Subject: Re: Binding energy by MM In-Reply-To: Message-ID: X-X-Sender: john@alpha2.bmc.uu.se MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: QUOTED-PRINTABLE Hi Ramon, you may want to take a look at the linear interaction energy (LIE) method introduced by =C5qvist et al., 1994 for calculating absolute free energies of binding. It is a semi-empirical method which is computationally less expensive than FEP. It is still similar to FEP in that it is based on thermodynamic cycles and includes thermal conformational sampling. However, the method involves only simulations of the two physical states (bound and free ligand) and requires no transformation processes. The method and some applications are described in: =C5qvist, J., Medina, C. and Samuelsson, J.E., Protein Eng., 7 (1994) 385= =2E =C5qvist, J. and Mowbray, S.L., J. Biol. Chem., 270 (1995) 9978. =C5qvist, J., J. Comp. Chem., 17 (1996) 1587. Hult=E9n, J., Bonham, N.M., Nillroth, U., Hansson, T., Zuccarello, G., Bouzide, A., =C5qvist, J., Classon, B., Danielsson, H., Karl=E9n, A., Kvarnstr=F6m, I., Samuelsson, B. and Hallberg, A., J. Med. Chem., 40 (1997) 885. Hansson, T. and =C5qvist, J., Protein Eng., 8 (1995) 1137. Hansson, T., Marelius, J. and =C5qvist, J., J. Comput.-Aided Mol. Design, 1998, in press. regards, John Marelius +-----------------------------------------------------------------+ | John Marelius | | Dept. of Molecular Biology, Uppsala University | | E-mail: john@xray.bmc.uu.se | | www: http://www.ibg.uu.se/~john | | address: Box 590, S-751 24 Uppsala, Sweden | +-----------------------------------------------------------------+ From katz@indigo.ucdavis.edu Tue Oct 14 13:30:36 1997 Received: from indigo.ucdavis.edu for katz@indigo.ucdavis.edu by www.ccl.net (8.8.3/950822.1) id MAA09810; Tue, 14 Oct 1997 12:35:51 -0400 (EDT) Received: from indigo.ucdavis.edu by indigo.ucdavis.edu via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for id JAA11095; Tue, 14 Oct 1997 09:37:30 -0700 Date: Tue, 14 Oct 1997 09:37:29 -0700 (PDT) From: Daniel Katz To: chemistry@www.ccl.net Subject: where are Alvarez's parameters? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I have been told that the program ehmacc (a program for extended Huckel molecular orbital calculations) uses parameters from Alvarez. Is there a published reference in which one can find Alvarez's parameters? Thanks. Daniel J. Katz UC Davis katz@indigo.ucdavis.edu From stavrev@hyper.com Tue Oct 14 14:30:38 1997 Received: from pp200.hyper.com for stavrev@hyper.com by www.ccl.net (8.8.3/950822.1) id OAA10621; Tue, 14 Oct 1997 14:24:38 -0400 (EDT) Received: by mail.hyper.com with Internet Mail Service (5.0.1457.3) id <47QSX9T1>; Tue, 14 Oct 1997 14:22:39 -0400 Message-ID: <25F54E6144ACD01190F2004033CA4BC20663AC@mail.hyper.com> From: "Stavrev, Krassimir" To: "'chemistry@www.ccl.net.'" Subject: RE: Absorption spectra from ZINDO/S Date: Tue, 14 Oct 1997 14:22:39 -0400 X-Priority: 3 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1457.3) Content-Type: text/plain; charset="iso-8859-1" Dear CCLers, The Zindo/S defaults in HyperChem were set long time ago, in accordance with the recommendations in the original papers by Ridley & Zerner, TCA 42 (1976) 223 and Bacon & Zerner TCA 53 (1979) 21. We have not performed studies on the influence of these factors on the electronic spectroscopy; we rather follow the original research of Dr. Zerner's group at the University of Florida. This strategy is outlined in bold in the HyperChem manuals where the variances of these factors are also discussed. Currently, the pi-pi interaction factor default in HyperChem is set to 0.585; the 0.64 value is recommended for triplets' spectroscopy. The latest version of HyperChem 5.02, downloadable also as an evaluation copy from www.hyper.com, utilizes this new default value. For more details, please see the July'97 discussion in the HyperChem newsgroup archive at www.hyper.com/support. Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice: (352) 371-7744/(800)-960-1871 Fax: 352-371-3662 From chem8@york.ac.uk Tue Oct 14 15:30:38 1997 Received: from pump2.york.ac.uk for chem8@york.ac.uk by www.ccl.net (8.8.3/950822.1) id PAA10821; Tue, 14 Oct 1997 15:04:23 -0400 (EDT) Received: from ebor.york.ac.uk (chem8@ebor.york.ac.uk [144.32.129.242]) by pump2.york.ac.uk (8.8.7/8.8.7) with SMTP id UAA27625 for ; Tue, 14 Oct 1997 20:04:20 +0100 (BST) Date: Tue, 14 Oct 1997 20:04:20 +0100 (BST) From: John Waite To: chemistry@www.ccl.net Subject: Recontact Greek graduate Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sorry to waste band-width - but will the Greek graduate, about to finish their Ph.D., who contacted me last week, please e-mail me as I now know of two positions that may be of interest. John Dr. John Waite, e-mail: chem8@york.ac.uk * or The National Hellenic Research Foundation,* john@john1.eie.gr Organic and Pharaceutical Chemistry Institute, phone: ++30-1-7238958 (direct) Vas. Konstantinou 48, phone: ++30-1-7247913(secrtry. Mary) Athens 116-35, fax: ++30-1-7247913 Greece or NCRS "Democritos", phone: ++30-1-6513112-5 X219 * c/o Dr. G.Kordas, e-mail john@john.nrcps.ariadne-t.gr Material Science Institute, Aghia Paraskevi, Attikis, Athens 153-10, Greece From martin@qtp.ufl.edu Tue Oct 14 17:30:41 1997 Received: from qtp.ufl.edu for martin@qtp.ufl.edu by www.ccl.net (8.8.3/950822.1) id QAA11194; Tue, 14 Oct 1997 16:37:15 -0400 (EDT) Received: from shadow.qtp.ufl.edu by qtp.ufl.edu (SMI-8.6/SMI-SVR4) id QAA06650; Tue, 14 Oct 1997 16:36:40 -0400 Received: by shadow.qtp.ufl.edu (SMI-8.6/SMI-SVR4) id QAA10960; Tue, 14 Oct 1997 16:36:45 -0400 Date: Tue, 14 Oct 1997 16:36:45 -0400 Message-Id: <199710142036.QAA10960@shadow.qtp.ufl.edu> From: Charles & To: "'chemistry@www.ccl.net.'" cc: martin@qtp.ufl.edu Subject: CCL:Absorption spectra from ZINDO/S Dear CCLers, > Following the discussion of the ZINDO/S interaction factors... While it is not possible to explain from first principles where the interaction factors come from in ZINDO, it is possibke to obtain ab initio interaction factors for pi-electron theory. Since the ZINDO method was originally derived using ideas from pi-electron theory, it may be helpful to understand exactly how pi-electron theory works to understand how to modify the ZINDO interactions. (BTW, the original idea for adjusting the pi-pi interaction factor in all-valence electron methods came from the work of Del Bene and Jaff'e (JCP vol 48, page 1807, 1968) - at least this is the earliest reference I know of. ) It is possible to derive the pi-pi interaction factor in semi-empirical pi-electron theory directly using Freed's ab initio Effective Valence Shell Hamiltonian theory. In particular, ths has recently been performed on a series of small, protonated Schiff bases in order to show how to properly reparameterize MNDO for MNDO-piCI calculations. The work on the MNDO-piCI calculations is currently under review, but you can find a preprint of it, along with some other details about the Effective Hamiltonian Calculations, on the Effective Hamiltonian Web Page (www.cat.syr.edu/~cmartin/hv). Again, note that this work rigorously applies to calculations using a pi-Full-CI or pi-SDCI and not the ZINDO all-valence-electron SCI, but some of the general ideas may transfer. For instance, in my opinion, it should be reasonble to adjust these interaction factors for a series of related compounds. By realted compounds, however, I mean that the excited states of these compounds should have similar character. For example, it might prove less usefull to use the same parameterization for protonated Schiff bases as for neutral polyenes because the excited states of neutral polyenes have much more ionic character than the protonated Schiff bases. (It may also be desirable to modify the one-center, two-electron Coloumb intergrals, as indicated by the Effective Hamiltonian Theory). Chuck Martin -- ------------------------------------------- Dr. Charles H. Martin Quantum Theory Project 362 Williamson Hall PO Box 118435 University of Florida Gainesville, Florida 32611-8435 Fax: (352) 392-8722 Email: martin@qtp.ufl.edu Web: www.cat.syr.edu/~cmartin/hv --------------------------------------------