From chemistry-request@server.ccl.net Fri Jul 21 03:24:49 2000 Received: from dns.campus.mlsultan.ac.za ([196.26.160.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA11635 for ; Fri, 21 Jul 2000 03:24:46 -0400 Received: from wpogate.mlsultan.ac.za (wpogate.campus.mlsultan.ac.za [196.13.102.11]) by dns.campus.mlsultan.ac.za (AIX4.2/UCB 8.7/8.7) with SMTP id JAA20160 for ; Fri, 21 Jul 2000 09:40:07 +0300 (USADT) Received: from MLSTGW-Message_Server by wpogate.mlsultan.ac.za with Novell_GroupWise; Fri, 21 Jul 2000 09:05:53 +0200 Message-Id: X-Mailer: Novell GroupWise 5.5.3 Date: Fri, 21 Jul 2000 09:05:28 +0200 From: "Thishana Singh" To: " Cc: Subject: G98 ONIOM Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id DAA11636 Dear Valentine, The article that Dr Reinaldo Pis Diez listed in his summary a few days ago was Dapprich and al., J.Molec.Struct.(Theochem) 461-462 (1999) 1-21 describing the g98's oniom implementation. I hope this helps. Regards Thishana Singh Department of Chemistry M L Sultan Technikon Durban South Africa From chemistry-request@server.ccl.net Fri Jul 21 04:09:00 2000 Received: from fluorid.ethz.ch (fluorid.ethz.ch [129.132.126.40]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA12041 for ; Fri, 21 Jul 2000 04:09:00 -0400 Received: from igc.phys.chem.ethz.ch (fluorid [129.132.126.40]) by fluorid.ethz.ch (8.8.8/8.8.8) with ESMTP id KAA05316 for ; Fri, 21 Jul 2000 10:09:05 +0200 (CEST) Sender: portmann@igc.phys.chem.ethz.ch Message-ID: <39780521.FF41C51D@igc.phys.chem.ethz.ch> Date: Fri, 21 Jul 2000 10:09:05 +0200 From: Stefan Portmann X-Mailer: Mozilla 4.61 [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: CCL CCL Subject: Quantum Chemistry Package with GUI Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello we have to think about a future solution for student classroom computers. In the quantum chemistry course we are currently using UNICHEM on SGI workstations. The new machines do not have to be SGI's necessarily again. I was already browsing the net to find UNICHEM like packages (should include a molecular editor) to run on other UNIX platforms (in particular LINUX) and was not very successful. On windows systems there are some options (Hyperchem, Titan). Does anybody know of something useful (commercial or freeware)? Thanks for you input Stefan -- Dr. Stefan Portmann Laboratory of Physical Chemistry ETH-Zurich Universitaetsstr. 65 CH-8092 Zurich Switzerland Phone: +41 (0) 1 632 57 82 Fax: +41 (0) 1 632 16 15 e-mail: portmann@igc.phys.chem.ethz.ch WWW: http://igc.ethz.ch/portmann From chemistry-request@server.ccl.net Fri Jul 21 01:43:58 2000 Received: from cal1.mantraonline.com ([202.56.204.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA11290 for ; Fri, 21 Jul 2000 01:43:55 -0400 Received: from cavewoman ([202.56.205.97]) by cal1.mantraonline.com (Netscape Messaging Server 4.1) with SMTP id FY22FU00.M1G; Fri, 21 Jul 2000 11:14:18 -0500 Message-ID: <001201bfe4be$0e7dae20$61cd38ca@cavewoman> From: "Rajarshi Guha" To: "Henry Pang" Cc: References: <20000721000557.33833.qmail@hotmail.com> Subject: Re: CCL:Seeing molecular orbitals? Date: Mon, 3 Jul 2000 11:19:30 +0530 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 > other. I think molecules are the beautiful building blocks of our Universe > and created for a purpose. I decline the view molecules are just chance > particles. I suspect from my reading of CCL, my intention may be seen as Hi, your comment suggests that somebody / something is making molecules to satisfy some aestheic urge. I fully agree that molecules are beutiful (in fact the shapes of organic molecules is what attracted me to chemistry when I was entering high school) - but I also think that they just happen to be beutiful. When you say that they are chance particles do you mean that they *just exist* ? I don't think so. Most things in the universe have a function to perform and they are made such that they perform it well - evolution. And so it also applies to molecules. In the case of molecules, performance for a function is not the only criterion - a more important (I think *most*) is geometry constraints - the molecule is what it is becuase of the way the bonds have to join! If it happens that this makes the molecule beautiful then be it - in th end you'll have to work the numbers and data that arise >from a molecule. Of course there should be a goal in the measurement and calculation of these data - measurement for measurementas sake is not very useful I think. At the same time somebody has to document the data - it might seem a pointless job, but when the data is put to use, the documenter will be able to sit back with a smile of satisfaction. In the end I think computational chemistry involves both kinds of work - getting, verifying and using data. In the midst of all this good looking molecules ;) makes the work fun! Bye, ================================== Rajarshi Guha Dept Of Chemistry IIT Kharagpur Email : rajarshi@presidency.com Web : www.psynet.net/jijog ================================== From chemistry-request@server.ccl.net Fri Jul 21 04:18:03 2000 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA12131 for ; Fri, 21 Jul 2000 04:18:03 -0400 Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3/8.9.3) with ESMTP id KAA23405; Fri, 21 Jul 2000 10:08:44 +0200 (MET DST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.44); 21 Jul 00 10:06:59 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.44); 21 Jul 00 10:06:54 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "Henry Pang" Date: Fri, 21 Jul 2000 10:06:37 +0100 Subject: Re: CCL:Seeing molecular orbitals? CC: CHEMISTRY@ccl.net Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <9444DC00A87@virgil.ruc.dk> Henry Pang: > I am new to computational chemistry. My background is medicine and human > ecology in Australia. Your post is the first indicator I have seen over a wide > range of CCL and books which signals caution. I am overwhelmed by the volume > and intensity of work on the methodology and mensuration of molecules, as if > that were the end in itself. No where do I see any concern for a Philosophy of > Computational Chemistry, which addresses just what is computational chemistry > and what its purpose might be in our Universe. I cannot believe the objective > is merely to measure everything and simply document these data? > > Even at my early stage, I am seriously pondering writing material jointly with > my academic supervisor who is a computational chemist, which sets out the link > (as I see it) between cosmology, quantum theory, relativity and higher > dimensions theory on the one hand and computational chemistry on the other. I > think molecules are the beautiful building blocks of our Universe and created > for a purpose. I decline the view molecules are just chance particles. I > suspect from my reading of CCL, my intention may be seen as revolutionary if > not outrageous and could well cause an uproar? Dear Henry, thank you for your comments. However, my little message "Seeing molecular orbitals?" was not intended to be highly philosophical. - The "molecular orbital" is a model concept, a one-electron wavefunction which serves as a convenient building block in the description of molecular many-electron states, but it is not an "observable" in the physical, quantum mechanical sense. In the molecular orbital approximation, the instantaneous correlation of the movements of the individual electrons is neglected; the electrons are allowed to "feel" each other only in an average manner. Hence, per definition, the molecular orbital has no "physical existence", no matter what you imply by the word 'existence'. 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.rub.ruc.dk/dis/chem/psos/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Fri Jul 21 04:21:42 2000 Received: from gensig.nibsc.ac.uk (gensig.nibsc.ac.uk [193.62.43.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA12151 for ; Fri, 21 Jul 2000 04:21:41 -0400 Received: from nibsc.ac.uk (dlinmf.nibsc.ac.uk [193.62.42.144]) by gensig.nibsc.ac.uk (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id JAA93590; Fri, 21 Jul 2000 09:20:29 +0100 (BST) Message-ID: <397808F1.D8ABF424@nibsc.ac.uk> Date: Fri, 21 Jul 2000 09:25:22 +0100 From: Mark Forster Organization: NIBSC X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: Francesca Ciccarelli , chemistry@server.ccl.net Subject: Re: hydrophobic bonds References: <3976C7C8.C2D5E5E0@cmns.mnegri.it> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Francesca If you wish I can send you a simple Perl script (pdb_hydrophobic.pl) which performs this task for protein PDB files. I could be easily be modified to include DNA. Mark Francesca Ciccarelli wrote: > Hi! > > I am looking for a way to detect hydrophobic interactions between two > amino acids or an amino acid and a DNA base reported in PDB complexes. > Can someone suggest to me how I can do? > > thanks in advance! > > francesca > > Francesca D. Ciccarelli, Pharm Chem D > Lab. of Experimental Oncology > Department of Cell Biology and Oncology > Consorzio Mario Negri Sud > 66030 Santa Maria Imbaro (Chieti), Italy > Phone: (39-0872) 570.292 > FAX: (39-0872) 570.412 > E-mail: ciccarel@cmns.mnegri.it > > *** Details on how to be removed from this list as well as an *** > *** archive of recent postings are available at *** > *** http://www.rcsb.org/pdb/forum.html *** -- Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel +44 (0)1707 654753 FAX +44 (0)1707 646730 E-mail mforster@nibsc.ac.uk From chemistry-request@server.ccl.net Fri Jul 21 08:33:34 2000 Received: from abacus.ac.BrockU.CA (abacus.ac.BrockU.CA [139.57.65.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA13922 for ; Fri, 21 Jul 2000 08:33:33 -0400 Received: from localhost (srothste@localhost) by abacus.ac.BrockU.CA (8.9.3/8.9.3) with SMTP id IAA87324; Fri, 21 Jul 2000 08:32:42 -0400 (EDT) Date: Fri, 21 Jul 2000 08:32:42 -0400 (EDT) From: "Stuart M. Rothstein" To: elewars cc: chemistry@ccl.net Subject: Re: CCL:PROGRAM FOR SCATTERPLOTS (STEREOSCOPIC?) In-Reply-To: <39776BAE.99ED3100@trentu.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr. Elewars: I can suggest an alternative method to solve your problem. By constructing histograms of the 'x', 'y', and 'z' variables, one can 'filter' those to see which values of 'x' (the 'clumps') are associated with those of 'y' and 'z'. This technique, 'histogram filtering', is described in: M. Snajdr, J.R. Dwyer, and S.M. Rothstein, J. Chem. Phys. 111 [22], 9971 (2000). For software, it only requires physica. Stuart M. Rothstein, Professor of Chemistry and Physics, Brock University, St. Catharines, Ontario, L2S 3A1 CANADA srothste@abacus.ac.brocku.ca http://chemiris.labs.brocku.ca/~chemweb/faculty/rothstein/ On Thu, 20 Jul 2000, elewars wrote: > Thursday 2000 July 20 > > > Hello, > > Suppose one has for, say, 50 molecules, 3 properties for each molecule > (e.g. dipole moment, frontier orbital gap, ionization energy--I just > made up these three merely as an example) and wishes to *see* if the > properties are correlated. You could create an x,y,z-type scatterplot > with a property for each axis and see how molecules with certain values > of the properties group themseves in certain parts of "property space". > Maybe there would be two or three well-defined clumps. If for each > molecule you have 4 properties you could add a fourth dimension to the > 3D plot by using color. > > QUESTIONS: > > 1) Is there a good program for creating attractive scatterplots? For > adding color and or a number (molecule #1, #2, etc.) to each point in > the plot? > > 2) Is there a program that will create *stereoscopic* 3D scatterplots > (for example, by showing two pictures that one can view with standard 3D > glasses), so that one can immediately see where in 3D space points lie? > > I suspect that programs like Maple and Mathematica can't do all this. > > Thanks > > E. Lewars > ========= > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Fri Jul 21 08:45:18 2000 Received: from nmr-v.ioc.ac.ru (root@nmr-v.ioc.ac.ru [193.233.3.213]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA13947 for ; Fri, 21 Jul 2000 08:44:08 -0400 Received: from localhost (val@localhost) by nmr-v.ioc.ac.ru (8.9.3/8.9.3) with ESMTP id QAA18615; Sun, 23 Jul 2000 16:46:52 +0400 Date: Sun, 23 Jul 2000 16:46:52 +0400 (MSD) From: Valentine Ananikov To: CHEMISTRY@ccl.net cc: fau@qtp.ufl.edu Subject: RE2:G98: ONIOM and Amber on TM systems Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Stefan and CCl members! Your description seems to be reasonable, but if one assumes so, this means that current G98 ONIOM implementation is not suitable at all for running oniom(ab-initio:Amaber) or oniom(ab-initio:AM1/PM3) calculations for transition metal containing systems. Moreover, very unlikely in the nearest future due to known difficulties of MM and semiempirical treatment of TM systems. Sounds a bit pessimistic. ( I know about UFF, but it does not seem to work well, especially for charged molecules) >From the other hand, in JPC 1996,100,19357 oniom(b3lyp:HF:MM3) calculations for platinum complexes are described. However, I am not aware of any MM3 parametrization for platinum. is there a way to repeat such calculations in G98? regards, Valentin. > Hi Valentine, > > The ONIOM method requires 3 calculations for > a molecule: a low level calc of the whole molecule > (ll/all), a low level calc of the high level part (ll/part) > and a high level calc of the high level part (hl/part). > The ONIOM energy is defined as > E(ONIOM) = E(ll/all) - E(ll/part) + E(hl/part) > > Although the low level energy contributions of the > high level part seem to cancel out, that is not > completely true. In order to have well behaved > high level parts, broken bonds are saturated with > hydrogen. This causes a difference in the MM > energy terms between ll/all and ll/part that reaches > at least three atoms inside the high level part > (dihedral angle with the saturation H). For that > reason (and programming reasons, I assume), > you need MM parameters for all atoms in the > molecule. > > In the last few days there was a thread concerning > ONIOM energies. One of the mails pointed to an > article that explains the ONIOM method in more > detail. > > Stefan > __________________________________________________________________ > Dr. Stefan Fau | fau@qtp.ufl.edu > ==================================================================== , , , , Valentine P. Ananikov |\\\\ ////| /////| NMR Group | \\\|/// | ///// | ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | Leninsky Prospect 47 | |===| | |===| | Moscow 117913 | | | | | | | Russia | | A | | | Z | | \ | | / | | / e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' Fax +7 (095)1355328 Phone +7 (095)9383536 ==================================================================== From chemistry-request@server.ccl.net Fri Jul 21 09:51:10 2000 Received: from UCONNVM.UConn.Edu (uconnvm.uconn.edu [137.99.26.3]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA14447 for ; Fri, 21 Jul 2000 09:51:10 -0400 Received: from nucleus.chem.uconn.edu [137.99.121.26] by UCONNVM.UConn.Edu (IBM VM SMTP V2R4a) via TCP with SMTP ; Fri, 21 Jul 2000 09:50:46 EDT X-Comment: UCONNVM.UConn.Edu: Mail was sent by nucleus.chem.uconn.edu Received: from NUCLEUS/SpoolDir by nucleus.chem.uconn.edu (Mercury 1.48); 21 Jul 00 09:48:59 -500 Received: from SpoolDir by NUCLEUS (Mercury 1.48); 21 Jul 00 09:48:46 -500 Received: from syr.edu (137.99.123.83) by nucleus.chem.uconn.edu (Mercury 1.48) with ESMTP; 21 Jul 00 09:48:44 -500 Message-ID: <39781DC8.3823B67C@syr.edu> Date: Fri, 21 Jul 2000 09:54:23 +0000 From: Deepak Singh Reply-To: desingh@syr.edu Organization: SU X-Mailer: Mozilla 4.73 (Macintosh; I; PPC) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: repository Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Hi Other than CCL, is anyone aware of a repository of computational (both quantum and classical) source code? These need not be complete programs, but rather standard algorithms and routines used commonly by the community. I have found a few web sites, but none totally satisfactory. Thanks Deepak. From chemistry-request@server.ccl.net Fri Jul 21 09:18:54 2000 Received: from bilbo.edu.uy (bilbo.edu.uy [164.73.160.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA14326 for ; Fri, 21 Jul 2000 09:18:41 -0400 Received: from localhost by bilbo.edu.uy (AIX 3.2/UCB 5.64/4.03) id AA22589; Fri, 21 Jul 2000 10:17:43 -0300 Date: Fri, 21 Jul 2000 10:17:42 -0300 (GRNLNDST) From: "Oscar N. Ventura" To: Stefan Portmann Cc: CCL CCL Subject: Re: CCL:Quantum Chemistry Package with GUI In-Reply-To: <39780521.FF41C51D@igc.phys.chem.ethz.ch> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Stefan: Wavefunction has a version of Spartan that runs under Linux, it's called Linux Spartan. Look at www.wavefun.com. O. ------------------------------------------------------------------------------- Prof.Dr.Oscar N. Ventura Tel.+(5982)9248396 Fax +(5982)9241906 MTC-Lab,Facultad de Quimica MTC-Lab http://bilbo.edu.uy/MTC-Lab.html Universidad de la Republica Gral.Flores 2124, C. C. 1157 All opinions are my own, and not Montevideo 11800, URUGUAY necessarily those of my employer "Violence is the last refuge of the incompetent." --- Salvor Hardin ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Jul 21 10:51:19 2000 Received: from coyote.iupui.edu (coyote.iupui.edu [134.68.220.82]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA14885 for ; Fri, 21 Jul 2000 10:51:18 -0400 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by coyote.iupui.edu (8.9.3/8.9.3/1.2IUPUIPO) with SMTP id JAA10713 for ; Fri, 21 Jul 2000 09:51:05 -0500 (EST) Message-ID: Date: 21 Jul 2000 10:05:39 -0500 From: "Boyd" Subject: re: repository To: "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Hi Deepak, One of the largest depositories of computational chemistry source code remains QCPE at Indiana University. http://qcpe.chem.indiana.edu/ Good luck, Don Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Editor, Journal of Molecular Graphics and Modelling (publication of the ACS COMP division and MGMS) http://chem.iupui.edu/~boyd/jmgm.html E-mail boyd@chem.iupui.edu From chemistry-request@server.ccl.net Fri Jul 21 11:17:09 2000 Received: from euch4e.chem.emory.edu (euch4e.chem.emory.edu [170.140.59.12]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA15083 for ; Fri, 21 Jul 2000 11:17:09 -0400 Received: from localhost (thom@localhost) by euch4e.chem.emory.edu (AIX4.2/UCB 8.7/8.7) with SMTP id LAA47582; Fri, 21 Jul 2000 11:15:39 -0400 (EDT) Date: Fri, 21 Jul 2000 11:15:38 -0400 (EDT) From: Thom Vreven Reply-To: Thom Vreven To: Valentine Ananikov cc: CHEMISTRY@ccl.net, fau@qtp.ufl.edu, Keiji Morokuma Subject: Re: CCL:RE2:G98: ONIOM and Amber on TM systems In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Valentine Ananikov, Indeed, at the moment it is not very easy to study TM using ONIOM(xx:MM) and ONIOM(xx:AM1/PM3). These two cases are a bit different, though. For the semiempirical methods, the high level region of the system must be well-defined with the low level method, and unavailable parameters for the TM pose a real problem. For ONIOM(xx:MM) combinations, there is a work-around. Of course, ideally one would be able to specify additional parameters in the input deck, but this is currently not possible. As mentioned in an earlier posting, MM bonded terms in the high level region that are further than 3 bonds away from the low level (MM) region cancel. This is simply the result of these terms being exactly the same in the MM model calculation and in the MM real system calculation, but of opposite signs in the ONIOM energy expression. The solution is to disconnect all the atoms in the model region that are further away then three bond from the MM region (whatever the parameters for those bonded terms are doesn't matter, so you might as well not include those bonded terms anyway). No bonds will be defined, and G98 will not protest that there are no parameters for those bonds (and associated angles). In order to do this, use the "Geom=Connectivity" keywords. Of course, atoms closer than three bonds to the MM region must not be disconnected. This solves the problem with the bonded terms correctly, but the Vanderwaals parameters for the TM are still missing. If the TM is quite far away from the MM region (which it will be, since it has to be at least three bonds anyway), the exact values of the VDW parameters hardly affect the results. Again, the MM VDW interactions within the high level region will cancel, and the VDW parameters of the TM are only used to describe the interaction of the high level layer with the low level layer. Just use something like "Fe-H-charge" as amber atomtype in G98, and effectively the VDW parameters of H will be used for Fe. Thom BTW. the 1996 ONIOM paper used a different implementation, where there was more flexibility to adjust MM parameters. ______________________________________________ Dr. Thom Vreven Chemistry Department 1515 Pierce Drive, Atlanta, Georgia 30322, USA Phone (404) 727-2381 Fax (404) 727-7412 E-mail thom@euch4e.chem.emory.edu ______________________________________________ On Sun, 23 Jul 2000, Valentine Ananikov wrote: > > > > Hi Stefan and CCl members! > > Your description seems to be reasonable, but if one assumes so, > this means that current G98 ONIOM implementation is not suitable > at all for running oniom(ab-initio:Amaber) or oniom(ab-initio:AM1/PM3) > calculations for transition metal containing systems. > Moreover, very unlikely in the nearest future due to known > difficulties of MM and semiempirical treatment of TM systems. > > Sounds a bit pessimistic. ( I know about UFF, but it does > not seem to work well, especially for charged molecules) > > >From the other hand, in JPC 1996,100,19357 oniom(b3lyp:HF:MM3) > calculations for platinum complexes are described. However, > I am not aware of any MM3 parametrization for platinum. > > is there a way to repeat such calculations in G98? > > > regards, Valentin. > > > > > Hi Valentine, > > > > The ONIOM method requires 3 calculations for > > a molecule: a low level calc of the whole molecule > > (ll/all), a low level calc of the high level part (ll/part) > > and a high level calc of the high level part (hl/part). > > The ONIOM energy is defined as > > E(ONIOM) = E(ll/all) - E(ll/part) + E(hl/part) > > > > Although the low level energy contributions of the > > high level part seem to cancel out, that is not > > completely true. In order to have well behaved > > high level parts, broken bonds are saturated with > > hydrogen. This causes a difference in the MM > > energy terms between ll/all and ll/part that reaches > > at least three atoms inside the high level part > > (dihedral angle with the saturation H). For that > > reason (and programming reasons, I assume), > > you need MM parameters for all atoms in the > > molecule. > > > > In the last few days there was a thread concerning > > ONIOM energies. One of the mails pointed to an > > article that explains the ONIOM method in more > > detail. > > > > Stefan > > __________________________________________________________________ > > Dr. Stefan Fau | fau@qtp.ufl.edu > > > > ==================================================================== > , , , , > Valentine P. Ananikov |\\\\ ////| /////| > NMR Group | \\\|/// | ///// | > ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | > Leninsky Prospect 47 | |===| | |===| | > Moscow 117913 | | | | | | | > Russia | | A | | | Z | | > \ | | / | | / > e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ > http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' > Fax +7 (095)1355328 Phone +7 (095)9383536 > ==================================================================== > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > > From chemistry-request@server.ccl.net Fri Jul 21 15:03:18 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA16024; Fri, 21 Jul 2000 15:03:18 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id PAA03386; Fri, 21 Jul 2000 15:03:18 -0400 (EDT) Date: Fri, 21 Jul 2000 15:03:17 -0400 (EDT) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: Dear CCL Subscribers -- Your coordinator has news... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Friends (you may not like me, but I like you, oh well... most of the time)... First... I am taking off for a month, and I will not be able to peek at CCL. This means: SEND ALL comments/special requests to team@ccl.net, so my dear associates can help you (or at least will do the best effort)... All other stuff goes where it was going before, i.e., to chemistry-request@ccl.net Do not sent anything to jkl@ccl.net, since I may, or may not have any Internet access, and even if I have, it will be over slow phone line, so be considerate... There is the second, more important issue: I need your comments on our supporting pages. When you start from http://www.ccl.net then click on "Supporting" under "About CCL" in the left navigation bar, or go directly to: http://www.ccl.net/chemistry/aboutccl/supporting You need a password to get there -- really easy. User ID: ccl Password: ccl Just type ccl twice in the boxes. It is password protected so only subscribers of CCL can look at it, and so it is not indexed via search engine robots. It is still a draft, and DO NOT SEND MONEY!!! (I know, you are all dying to send me cash, but hold for a month, please...). I need to be in town to process the income, so PLEASE WAIT UNTIL I AM BACK. I have a few great favors to ask. Please send mail to team@ccl.net. 1) Comment on the supporting pages, tell us how to make them more persuasive, so people will give CCL their last pair of pants (yes, I am kidding...). 2) Tell me if you will be supporting CCL. You do not have to... I value your participation. You do not have to support CCL to access CCL Web site and participate as a subscriber. However, I HAVE TO KNOW, IF I CAN COUNT ON ANY SUPPORT FROM YOU!!! CCL is free and should stay this way, since its success is broad participation. 3) Tell us about new, possible ways of supporting CCL. Note, we are giving you something in exchange. The UNIX account, CDs with archives, or exposure, are all quite tangible benefits. We do not want to beg, we want to earn it. If you know about some other attractive ways of supporting CCL, let us know. We really want CCL to stay forever, and it will only happen if it can pay its bills, and has some rainy day fund. 4) Please, consider supporting CCL. If I do not have a grass-root support, I am not sure how I will be able to sustain CCL in a long run. OSC helps a lot and is supporting CCL through all these years. But it would be SO MUCH EASIER FOR ME AND MY STUDENTS to know that CCL has a security cushion. Note, I am not paid a penny for managing CCL. This is good and bad... I can claim that it is my community service. But at the same time, I cannot say that maintaining CCL is a priority. If it does not pay my salary, it is not in my job description. It is that simple. 5) Please consider supporting CCL. I could hire more students, and more experienced students (e.g., Graduate Research Assistants), if I had some control over the CCL budget. CCL is not free... CCL actually costs OSC a good chunk of cash. I feel uneasy requesting CCL support from my management, because I have to prove again and again that it is a useful site and it is needed for our users. But eventually the taxpayer supports the CCL. And taxpayer (who elects politicians, who select supervisory bodies) may say "No". I strive to keep CCL an international community, but it is US taxpayer who pays the bill. 6) Please consider supporting CCL. Only if you are supporting CCL, we have a clue that what we do here is useful and that CCL has value. I know that you need it, since you use it. We have a lot of hits to our archives, the CCL discussions are going on for more than 9 years now. Those who post to CCL, or who provide us with free software to CCL archives are the real heros. Without them, there would be no CCL in the first place. However, some of you may be getting more than you give. Please consider support CCL. Found a job? Found a good postdoc? Found a good literature reference? Got a clue how to solve it after searching CCL archives? Do a fast calculation, and check how much you would have to pay for a head hunter, for an advertisement in the journal, for searching commercial databases, or for hiring a consultant... These are only examples... I did not mention software archives, finding people, learning what is hot, and what is not, etc., etc... So, please let us know what we need to do to get some support, and consider supporting CCL. Try all the forms and pages, tell us how to improve them, and we will do... Yours Jan Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Fri Jul 21 17:35:02 2000 Received: from prserv.net (out2.prserv.net [32.97.166.32]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA16775 for ; Fri, 21 Jul 2000 17:35:01 -0400 From: jmmckel@attglobal.net Received: from attglobal.net ([32.101.203.137]) by prserv.net (out2) with SMTP id <200007212134092290306867e>; Fri, 21 Jul 2000 21:34:10 +0000 Message-ID: <3978C0E8.2E9F2BE6@attglobal.net> Date: Fri, 21 Jul 2000 16:30:16 -0500 Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.51 [en]C-CCK-MCD (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: Marcel Swart CC: CHEMISTRY@ccl.net Subject: Re: CCL:DFT & metal metal bonds References: <200007200722.JAA66801@zisgi.unizh.ch> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I recall using the relativistic ECP's in deMon [also in DGAUSS] for the Ag dimer. The 17 valence ECP was better than the 11 or 1 electron ECP's, and was better than all the all electron non-relativistic results. John McKelvey Marcel Swart wrote: > >You want to elaborate on this? Is it because of the STOs? As to GTO's I > >use TZVP/P basis sets, which are not too bad usually. > > Yes, the STO's are always much better. But not only that. It is a > very clever program, making the calculations very efficient when > looking at CPU-time, parallellization, those kind of things. > > > > Furthermore, did you also include relativistic effects ? > > > >yes, scalar relativistic via the ECP. > > Well, that's not really what I meant. You assume that the ECP's mimic > the relativistic effects you are after, but it is not the same as > including the relativistic effects themselves !!! > > > > I guess when you look at Tungsten/Molybdenum, these can be quite > >significant. > >> Again this is a YES to ADF, since in this program these effects are > > > easily taken into account. > > Also, I know from work from my Professor (yet unpublished I think), > who is an expert in Relativistic Quantum Chemistry (J.G. Snijders), > that these relativistic effects are needed for heavy atom dimers. If > you don't include them (properly), the calculations are not > performing very well. > > Marcel. > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net