From cletner@remcure.bmb.wright.edu Wed Feb 23 00:02:40 1994 Received: from remcure.bmb.wright.edu for cletner@remcure.bmb.wright.edu by www.ccl.net (8.6.4/930601.1506) id XAA06943; Tue, 22 Feb 1994 23:43:09 -0500 Received: by remcure.bmb.wright.edu (920330.SGI/921111.SGI.AUTO) for CHEMISTRY@ccl.net id AA07445; Tue, 22 Feb 94 23:42:17 -0800 Date: Tue, 22 Feb 1994 23:32:19 -0800 (PST) From: Charles Letner Subject: Amber and Sybyl on a Cray Y-MP8/864 To: Computational Chemistry List Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello everyone, I'm working on a grant for time on a Cray to perform molecular dynamics calculations. Does anybody have any information comparing Amber and Sybyl(versions 4.0 and 5.7 I think) in terms of vectorization? I could also use any information on benchmarks between the programs in terms of efficiency. Any information you can provide will be greatly appreciated. I would also be interested in information comparing these two on other platforms. Thanks Chuck Charles Letner Wright State University Department of Biochemistry Dayton, OH 45435 e-mail: cletner@remcure.bmb.wright.edu From elcana@iqm.unicamp.br Wed Feb 23 09:02:47 1994 Received: from nyx.iqm.unicamp.br for elcana@iqm.unicamp.br by www.ccl.net (8.6.4/930601.1506) id IAA09648; Wed, 23 Feb 1994 08:14:19 -0500 Received: from localhost (elcana@localhost) by nyx.iqm.unicamp.br (8.6.4/8.3) id SAA02267; Tue, 22 Feb 1994 18:46:03 -0300 From: Anselmo Elcana de Oliveira Message-Id: <199402222146.SAA02267@nyx.iqm.unicamp.br> Subject: IR intensities To: chemistry@ccl.net Date: Tue, 22 Feb 1994 18:46:00 -0300 (GMT-3:00) X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 269 Hi netters! I'm searching for references of infrared intensities in Si-compounds. Thanks in advance. Anselmo Elcana de Oliveira Departamento de Fisico-Quimica Instituto de Quimica Unicamp Campinas -SP Brazil email: ELCANA@STYX.IQM.UNICAMP.BR From chp1aa@surrey.ac.uk Wed Feb 23 11:02:53 1994 Received: from sun2.nsfnet-relay.ac.uk for chp1aa@surrey.ac.uk by www.ccl.net (8.6.4/930601.1506) id KAA11685; Wed, 23 Feb 1994 10:42:02 -0500 Via: uk.ac.surrey; Wed, 23 Feb 1994 15:41:09 +0000 Via: central.surrey.ac.uk; Wed, 23 Feb 94 15:41:04 GMT Received: by central.surrey.ac.uk (1.37.109.8/16.2) id AA17597; Wed, 23 Feb 1994 15:41:03 GMT From: Mr Andrew D Allen Message-Id: <9402231541.AA17597@central.surrey.ac.uk> Subject: Homology: Studies To: chemistry@ccl.net Date: Wed, 23 Feb 94 15:41:02 GMT Mailer: Elm [revision: 70.85] As promised here is the summary of replies on Homology studies. ################################################################################ >From major@dino.qci.bioch.bcm.tmc.edu Tue Feb 22 14:14 GMT 1994 HOMOLOGY by Biosym (San Diego, CA) has an integrated package to search sequence databases and make homology 3D model. I have used it for several years with satisfaction. _____________________________________________________________________ Joseph G. Major, Ph.D. major@qci.bioch.bcm.tmc.edu (713)664-2288 (voice) (713)664-8914 (fax) ################################################################################ >From KOEHLER@IRBM.IT Fri Feb 18 19:06 GMT 1994 Dear Mr. Allen: There is plenty of code to do standard 1D/1D peptide sequence matching which dates back to the Needleman-Wunsch algorithm.[1] One package which contains several variations of this matching algorithm is the GCG software.[2] [1] Needleman, S. B.; Wunsch, C. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 1970, 48, 444-453. [2] Genetics Computer Group, (1991), Program Manual for the GCG Package, Version 7, April 1991, 575 Science Drive, Madison, Wisconsin, USA 53711. More recently, there has been a great deal of interest in methods for finding which 3D protein structure is compatible with a given 1D sequence (the inverse protein folding problem). This software is potentially useful for finding structures which despite their low primary sequence homology, nevertheless share similar protein folds. Below is a summary of the responses to my query to the bionet.biology.computational mail newsgroup (comp-bio@dl.ac.uk). Below is a summary of publicly or commercially available sequence/structure matching software. I apologize in advance for any omissions or errors. Thanks to all that replied, especially Steve Bryant, Steve Brenner, Gordon Crippen, Vladimir Maiorov, and David Eisenberg. 1) Brenner (seb1005@mbfs.bio.cam.ac.uk) plans to make software available "once it's stable" 2) Bryant (bryant@melanie.nlm.nih.gov), Lawrence The Bryant threading software is available via anonymous ftp from ncbi.nlm.nih.gov (130.14.25.1) in the compressed tar archive /pub/pkb/Threading.tar.Z. 3) Blundell, Donnelly, Eisenmenger, Johnson, Overington, Sali, Topham, Blundell's Composer software is available from Tripos Associates however the Blundell's sequence/structure software is currently not available. 4) Crippen (crip@phar.umich.edu), Maiorov (wowa@phar.umich.edu) Crippen and Maiorov's contact potential software may be obtained by writing Vladimir Maiorov. 5) Eisenberg (david@uclaue.mbi.ucla.edu), Bowie, Choe, Luthy, McLachlan, Mcleod, Wesson, Wilmanns, Yamashita Academics may obtain the 3D Structures Profile software by writing David Eisenberg. Commercial sites may obtain this software through Biosymm. 6) Jones (jones@bsm.bioc.ucl.ac.uk), Taylor, Thornton plans to make it available, but not ready yet 7) Ouounis, Sander, Scharf, Schneider no information 8) Sippl, Casari, Floeckner, Froschauer, Gottsbacher, Hendlich, Lackner, Weitckus no information 9) Skolnick, Godzik, Kolinski Sknolnick's MatchMaker software will be available from Tripos Associates. The following excellent reviews compare and contrast the various methods available for sequence/structure matching. (1) Wodak, S. J.; Rooman, M. J. Generation and testing protein folds. Curr. Opinion Struct. Biol. 1993, 3, 247-259. (2) Fetrow, J. S.; Bryant, S. H. New programs for protein tertiary structure prediction. Bio/Technology 1993, 11, 479-484. I hope you find the above information useful. Sincerely, ------------------------------------------------------------------ | Konrad Koehler | Computational Chemistry Group | | internet: koehler@irbm.it | Department of Medicinal Chemistry | | | IRBM | | telephone: +39-6-910-93606 | Via Pontina Km. 30,600 | | fax: +39-6-910-93225 | 00040 Pomezia (Roma) | | | Italy | ------------------------------------------------------------------ ################################################################################ >From raman@bioc01.uthscsa.edu Fri Feb 18 19:11 GMT 1994 Andy: There are many ways you could achieve this: 1. BLAST server 2. FASTA protocol 3. Server in Heidelberg You can obtain information on 1 & 2 by setting your gopher client to any of the biology gophers (e.g. fly.bio.indiana.edu). I like 3, since it not only provides the homology, but also the secondary structure prediction. This server is maintained by Chris Sander's group at EMBL, Heidelberg. To get instructions on using the server do the following: send email to the following address with no subject field: predictprotein@embl-heidelberg.de just include the word "help" in the body of the message. Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry c.raman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** ################################################################################ >From richards@msicam.co.uk Mon Feb 21 16:37 GMT 1994 Hi Andy, Standard rationale for getting 3D structures from sequence usually involve 1) database search of primary sequences (Brookhaven have some facilities for this) 2) alignment of "best score" sequences (use FASTA, SOMAP etc.) 3) modelling of chunks or unknown sequence onto the 3D shapes of homologous proteins 4) annealing unknown coordinates to "stitch together" all the residues to make a final 3D model 5) refinement and minimization/dynamics Quanta/CHARMm have , believe it or not, all of steps 1 to 5! You can scan your structure database and get back "best hits". Use FASTA to align multiple sequences (usually around 5 at once). Then replace unknown coordinates bit by bit (based on the best homologous structure/sequence). The annealing is done by CHARMm and you tweak the refinement using rotamer libraries to place your sidechains. Then finish off with CHARMm for the final minimization. Let me know if you need any help in setting up your files etc. to automate your database searching/alignments. Richard ################################################################################ >From nittoli@pokey.chem.sunysb.edu Mon Feb 21 18:03 GMT 1994 Hi Andy, I know of two commercial programs that can do what your colleague desires. One is COMPOSER, part of SYBYL (Tripos, St. Louis, MO, USA) and the other is HOMOLOGY, part of Insight (BioSym, San Diego, CA, USA). COMPOSER is based on T. Blundell's work (Eur. J. Biochem., 172:513-520 (1988)) and HOMOLOGY is based on J. Greer's work (J. Mol. Biol., 153:1027-1042 (1981)). It is important to know the phylogenetic relationship among other known 3D proteins in order to do this type of modelling. Good luck, Thomas Nittoli Dept. of Chemistry State University of NY Stony Brook, NY 11794-3400 USA Phone: (516)632-7854 FAX: (516)632-7960 Internet: nittoli@pokey.chem.sunysb.edu From yverband@vnet3.vub.ac.be Wed Feb 23 13:02:53 1994 Received: from mahler.belnet.be for yverband@vnet3.vub.ac.be by www.ccl.net (8.6.4/930601.1506) id MAA14038; Wed, 23 Feb 1994 12:51:14 -0500 Received: from rc1.vub.ac.be by mahler.belnet.be with SMTP (PP); Wed, 23 Feb 1994 18:51:05 +0100 Received: from vnet3.vub.ac.be by rc1.vub.ac.be (4.1/RC1-931231) id AA18827; Wed, 23 Feb 94 18:55:13 +0100 Received: from [134.184.47.231] (alnafpmc231) by vnet3.vub.ac.be (4.1/VUB.920213) id AA28015; Wed, 23 Feb 94 18:55:09 +0100 Message-Id: <9402231755.AA28015@vnet3.vub.ac.be> Date: Wed, 23 Feb 1994 18:51:49 -0800 To: CHEMISTRY@ccl.net From: yverband@vnet3.vub.ac.be (Yves Verbandt) Subject: thiophene oligomer Dear Netters, As I am involved in study of the optical properties of the oligomers of thiophene and phenyl, I would like to ask a question about the heptamer (n=7) of oligothiophene. Can anyone provide me (a literature reference is ok) with information on the geometry of this molecule in the following situations : 1) isolated molecule 2) molecule in 1-propanol (at different temperatures) 3) molecule in a nonpolar solvent 4) molecule in in PMMA (solid state) Thanking you in advance, I will be glad to provide a summary to the list. Yours sincerely, ========================================================================== Yves Verbandt tel. 32-2-641.36.13 Applied Physics Dept. fax. 34.50 Vrije Universiteit Brussel email yverband@vnet3.vub.ac.be Pleinlaan 2, 1050 Brussel, BELGIUM yverband@vub.ac.be ========================================================================== From pmr1716@ggr.co.uk Wed Feb 23 14:04:19 1994 Received: from gate.ggr.co.uk for pmr1716@ggr.co.uk by www.ccl.net (8.6.4/930601.1506) id NAA14645; Wed, 23 Feb 1994 13:46:19 -0500 Received: from mailhub.ggr.co.uk by gate.ggr.co.uk; Wed, 23 Feb 1994 18:44:37 GMT Received: from ukwbf07 by mailhub.ggr.co.uk; Wed, 23 Feb 1994 18:42:13 GMT Received: from localhost by ukwbf07 (8.6.4/imd160294) id SAA01980; Wed, 23 Feb 1994 18:55:19 GMT Date: Wed, 23 Feb 1994 18:55:18 +0000 (GMT) From: Murray-Rust Dr P Subject: Collaborative software development To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I gather you have just had a discussion on this newsgroup about the use of C++ - we have had a similar one on bionet.software. I'm not intending to re-open the discussion (which I didn't read at the time, but have had mailed to me), but to ask for help from those of you who believe in a collaborative, tool-based, approach to software development. I believe that it is now possible to get a relatively unstructured group of netters who, communally, develop fundamental tools (not programs) for certain parts of scientific computation (e.g. bioinformatics and the related part of computational chemistry). I hope to set this going in the next week or two by posting (probably at Daresbury) various tools that I have written. Hopefully these can act as a nucleus which will accrete other voluntary contributions. There are several categories of tools - not all yet very well populated - such as: a C++ class library tcl scripts and tk gui's tools for using CIF, not just for crystallography but as a generic mechanism for handling many file types and creating simple *portable* container classes (specifically arrays and heterogeneous compound objects) navigational aids (esp. html/www) In addition it would be useful to have: collections of read-only data (such as the connexion tables for amino acids; atomic weights, etc) manuals and examples of well-defined file formats The present major component is a set of C++ routines for some basic aspects of bioinformatics. Examples are: reading/writing various file formats, PDB, CIF, sequence entries; molecular geometry; and a considerable amount of basic housekeeping (dynamic arrays, text parsing, etc)). This has been designed (or at least has evolved!) to support extensibility in a distributed community. It also has an automatic documenting system which produces structured html pages from the *.h files (if written in an appropriate manner) and a large set of test routines and examples. I'd be very grateful for anyone who would like to test a beta version of this. It's been developed on g++, CC (cfront on IRIS), and Borland 3.0. My experience is that C++ is not totally portable at present, especially in *loading*. I have *not* used templates since although I can get them to compile and run sometimes, I find it difficult to get the same code running on all three platforms. (I use the macro method instead). Besides helping with installation it is important to get feedback on whether the style and documentation are helpful. A major concern I have is for navigation. I have sometimes found other people's C++ libraries often take quite a bit of time getting into. Therefore the use of html (you will need a clinet/browser such as mosaic, though lynx would do) is critical. I am also thinking about the best "rules" or constitution for a self-help exercise like this. Control of the namespace is important since otherwise the project degenerates into incompatible regions, but informal extensibility is needed or the project won't live. I have at least two experiences which make me optimistic that it will work. The first is the way that many computational groups flourish (I'm partcularly familiar with tcl.comp.lang where high-quality tools are developed and added at frequent intervals); and secondly the development of the STAR/CIF dictionaries and tools by the crystallographic community. DISCLAIMER: I have used these tools, inter alia, for teaching at MSc level at Birkbeck College. Neither Birkbeck, nor my employers Glaxo, is formally responsible for the contents of this message, nor for the software described, though they are aware of my intention to make them public. ------------------------------------------------------------------------------ Peter Murray-Rust | "Nothing exists except atoms and empty pmr1716@ggr.co.uk | space; all else is opinion" (Democritos). Protein Structure, Glaxo Research & Development, Greenford, MIDDX, UB6 0HE, UK ------------------------------------------------------------------------------ From suzi@vitus.ucdavis.edu Wed Feb 23 15:03:01 1994 Received: from ucdavis.ucdavis.edu for suzi@vitus.ucdavis.edu by www.ccl.net (8.6.4/930601.1506) id OAA15249; Wed, 23 Feb 1994 14:40:37 -0500 Received: from vitus.ucdavis.EDU by ucdavis.ucdavis.edu (8.6.5/UCD2.50) id LAA09943; Wed, 23 Feb 1994 11:35:05 -0800 Received: by vitus.ucdavis.EDU (930416.SGI/UCD2.02) id AA28815; Thu, 24 Feb 94 11:37:42 -0800 From: suzi@vitus.ucdavis.edu (Susan C. Tucker) Date: Thu, 24 Feb 94 11:37:42 -0800 Message-Id: <9402241937.AA28815@vitus.ucdavis.EDU> To: chemistry@ccl.net Subject: email addrs, Tomasi SCRF model Hi, We would like to perform some calculations using J. Tomasi's SCRF continuum solvent model (Miertus,Scrocco and Tomasi, Chem Phys 55,117(1981)), which has been incorporated into at least one version of the MONSTERGAUSS program. Note that this is Not the Kirkwood-Onsager SCRF method (ideal dipole in a spherical cavity) which has also been implemented in other versions of the MONSTERGAUSS program, as well as in Gaussian 92. We are looking for information about how to obtain the MONSTERGAUSS program containing Tomasi's method and/or email or fax addresses for J. Tomasi or Juan Bertran. Thanks so much for your assistance. Suzi Tucker sctucker@ucdavis.edu Dept. of Chemistry UC Davis From noy@tci002.uibk.ac.at Wed Feb 23 15:06:50 1994 Received: from uibk.ac.at for noy@tci002.uibk.ac.at by www.ccl.net (8.6.4/930601.1506) id OAA15258; Wed, 23 Feb 1994 14:41:01 -0500 Received: from tci002.uibk.ac.at by uibk.ac.at with SMTP id AA16645 (5.65c/IDA-1.4.4 for ); Wed, 23 Feb 1994 20:40:52 +0100 Received: by tci002.uibk.ac.at (AIX 3.2/UCB 5.64/CFIBK-2e.AIX) id AA13063; Wed, 23 Feb 1994 20:40:48 +0100 From: noy@tci002.uibk.ac.at (Teerakiat Kerdcharoen) Message-Id: <9402231940.AA13063@tci002.uibk.ac.at> Subject: solvation no. from MD & MC To: chemistry@ccl.net Date: Wed, 23 Feb 1994 20:40:48 +0100 (NFT) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 882 Dear computational chemists, I have a question about the coordination number obtained >from MD and MC simulations. Let me give an example of a cation in hydration shell. The cation has a resident time which no water exchange occurs within this period. Most MD simulations ( mostly within a few picoseconds ) can give only an exact value of coordination number. For example, hydration number of 6 is given. In the other hand, MC, with time-independence and truly statistically, could probably gives the coordination number closer to the experiment which the observation time is much more than an MD. MC can also give percentual distribution of coordination numbers ( not exactly 6 ,i.e, 98% for 6, 1.2 % for 7 and 0.8% for 5 ). Is it true ? Any comments and ideas would be greatly appreciated. yours truly, Teerakiat --- Teerakiat Kerdcharoen noy@tci2.uibk.ac.at From noy@tci002.uibk.ac.at Wed Feb 23 16:03:04 1994 Received: from uibk.ac.at for noy@tci002.uibk.ac.at by www.ccl.net (8.6.4/930601.1506) id PAA15623; Wed, 23 Feb 1994 15:05:25 -0500 Received: from tci002.uibk.ac.at by uibk.ac.at with SMTP id AA16886 (5.65c/IDA-1.4.4 for ); Wed, 23 Feb 1994 21:04:59 +0100 Received: by tci002.uibk.ac.at (AIX 3.2/UCB 5.64/CFIBK-2e.AIX) id AA23591; Wed, 23 Feb 1994 21:04:55 +0100 From: noy@tci002.uibk.ac.at (Teerakiat Kerdcharoen) Message-Id: <9402232004.AA23591@tci002.uibk.ac.at> Subject: Re: CCL:ab initio Pair Potentials.MD or MC program? To: jamejias@obelix.cica.es Date: Wed, 23 Feb 1994 21:04:55 +0100 (NFT) Cc: chemistry@ccl.net In-Reply-To: <9402221957.AA20386@obelix.cica.es> from "jamejias@obelix.cica.es" at Feb 22, 94 08:57:43 pm X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 1526 : I am working on the obtention of pair potentials from ab initio : embedded cluster calculations. I would like to test these pair : potentials but actually I haven't any code to do Molecular Dynamics : or Monte Carlo simulations of solids (bulk or/and surfaces). Does : somebody know about some freely distributed program which allows : to do such simulations? Dear sir, Sorry to reply to the lists since someone may be interested. A good MD program freely available on internet called Moldy may be of some values for you. The program is well-documented and well structural programmed. It can run on Unix, Cray and VMS. The potential could be easily changed inside the program. It supports many features i.e. Ewald long-range corrections, RDF. I believe that it can perform simulations in solid phase. The program can be reached via anonymous FTP at earth.ox.ac.uk /pub/moldy The author is Keith Refson keith@earth.ox.ac.uk sincerely, Teerakiat ---------------------------------------------------------------------------- Teerakiat Kerdcharoen (NOY) Institute of General and Inorganic and Theoretical Chemistry Innrain 52a, A-6020 Innsbruck AUSTRIA e-mail: noy@tci.uibk.ac.at, noy@tci2.uibk.ac.at, c72454@cx.uibk.ac.at : noy@atc.atccu.chula.ac.th, noy@atc2.atccu.chula.ac.th ( Bangkok ) Research : Molecular Dynamics simulations : Computer Aided Molecular/Material Designs ----------------------------------------------------------------------------- From topper@magnum.cooper.edu Wed Feb 23 17:02:56 1994 Received: from magnum.cooper.edu for topper@magnum.cooper.edu by www.ccl.net (8.6.4/930601.1506) id QAA16754; Wed, 23 Feb 1994 16:30:51 -0500 Received: by magnum.cooper.edu id AA03028 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Wed, 23 Feb 1994 16:32:10 -0500 Date: Wed, 23 Feb 1994 16:32:10 -0500 From: Robert_Topper Message-Id: <199402232132.AA03028@magnum.cooper.edu> To: chemistry@ccl.net, noy@tci002.uibk.ac.at Subject: Re: CCL:solvation no. from MD & MC Oh no! A Monte Carlo vs. MD debate!! Speaking as someone who has a little working familiarity with both techniques...I'm as unqualified to answer this as anyone. And completely unbiased (NOT). It seems like the issue is whether the MD or MC calculation is converged or not with respect to the computation of equilibrium properties. In principle, if steps are taken to ensure that the MD simulation is ergodic, the MD and MC methods will converge to the same equilibrium properties. In the limit of infinite sampling you are guaranteed this with MC, but not with MD unless you use some of the standard, elegant tricks to randomize things a bit. Of course, when the sample is finite you have no guarantee that either method will be completely ergodic. In Monte Carlo-land this is called "quasi-ergodicity." Perhaps in MD-land too. I hope this note is at least entertaining, because it certainly doesn't answer the implied question...namely, which method is better / more appropriate for your particular application. My own personal bias screams "Use MD for info on the time-dependence and MC for equilibrium properties," but there are plenty of useful ways to use MD to calculate equilibrium properties. Hopefully this is of some help to you - Allen and Tildesley present nice discussions of MD vs. MC in their book "Computer Simulations of Liquids." -Robert ******************************************* Robert Q. Topper Assistant Professor of Physical Chemistry The Cooper Union for the Advancement of Science and Art Cooper Square New York, NY 10003 topper@magnum.cooper.edu (212)353-4378 FAX:(212)353-4341 ************************************************************************ ************************************************************************ * The Cooper Union for the Advancement of Science and Art, established * * by Peter Cooper in 1859, is a private institution of higher learning * * where all students receive full-tuition scholarships. * ************************************************************************ ************************************************************************ From KUS%SUEARN2.BITNET@mps.ohio-state.edu Wed Feb 23 15:30:55 1994 Received: from ohstpw.mps.ohio-state.edu for KUS%SUEARN2.BITNET@mps.ohio-state.edu by www.ccl.net (8.6.4/930601.1506) id PAA15948; Wed, 23 Feb 1994 15:30:54 -0500 Received: from SUEARN2.BITNET (MAILER@SUEARN2) by MPS.OHIO-STATE.EDU (PMDF V4.2-14 #3557) id <01H98ACMGCJK8WXYKY@MPS.OHIO-STATE.EDU>; Wed, 23 Feb 1994 15:30:49 EST Date: Wed, 23 Feb 94 21:40 MSK From: Mikhail Kuzminsky -135-6388 (095) Subject: Re: CCL:Cu/Ag/Au To: CHEMISTRY@ccl.net Message-id: <01H98ACOGYCM8WXYKY@MPS.OHIO-STATE.EDU> Content-transfer-encoding: 7BIT Status: RO > Recently i got involved in some combined experimental and theoretical > work on small liganded Cu/Ag/Au cations. I am using standard ab initio > techniques with different pseudopotential parametrizations. In order to > avoid errors and/or incompletenes in the reference list I would appreciate > to point me to publications in this field. I tryed some literature data > bases, however, the results are poor. By my opinion,for calculations with medium-size basis may be good non-local pseudopotential by Y.Sakai e.a. . If i am correct,it was published in Y.Sakai,E.Miyoshi,M.Klobukowski,S.Huzinaga,J.Comp.Chem.,1987,v.8,N3, p.226-264 (unfortunally i can't check it because our shop don't have this journal :-( ). Some years ago we used this pseudopotential for study of some Cu-contained compounds,but then we didn't have any experience. Mikhail Kuzminsky, Institute of Organic Chemistry,Moscow e-mail : KUS@SUEARN2.BITNET From jle@world.std.com Wed Feb 23 20:02:54 1994 Received: from news.std.com for jle@world.std.com by www.ccl.net (8.6.4/930601.1506) id TAA18423; Wed, 23 Feb 1994 19:49:12 -0500 Received: from world.std.com by news.std.com (5.65c/Spike-2.1) id AA28792; Wed, 23 Feb 1994 19:49:10 -0500 Received: by world.std.com (5.65c/Spike-2.0) id AA14386; Wed, 23 Feb 1994 19:49:08 -0500 Date: Wed, 23 Feb 1994 19:49:08 -0500 From: jle@world.std.com (Joe M Leonard) Message-Id: <199402240049.AA14386@world.std.com> To: chemistry@ccl.net Subject: Missing Sybyl params - where found? Folks, Is there a repository or body of literature for Sybyl FF parameters out there? I know there's been scads of interest in generating missing MM2 parameters over the years, but I'm interested in whether there's been similar work with Sybyl... Examples of missing params are things like S-H, Si-H, P-H... I know there's a mechanism for handling params that are totally absent. In this case, the ??-H params are falling under the *-H default parameter of 1.008 - which is not really useful for these larger atoms. I would rather find a set of "appropved" or "semi-approved" params before going off and generating some new ones on my own. Thanks in advance! Joe Leonard jle@world.std.com From pis_diez@cpd.uva.es Wed Feb 23 23:02:56 1994 Received: from relay.rediris.es for pis_diez@cpd.uva.es by www.ccl.net (8.6.4/930601.1506) id WAA19411; Wed, 23 Feb 1994 22:44:46 -0500 Received: from rediris.es by relay.rediris.es (PMDF V4.2-11 #4193) id <01H9837CK1Z48WW9CD@relay.rediris.es>; Wed, 23 Feb 1994 12:07:37 GMT+1 X400-Received: by mta iris-dcp in /PRMD=iris/ADMD=mensatex/C=es/; Relayed; Wed, 23 Feb 1994 12:07:29 UTC+0100 X400-Received: by /PRMD=iris/ADMD=mensatex/C=es/; Relayed; Wed, 23 Feb 1994 11:57:39 UTC+0100 Date: Wed, 23 Feb 1994 11:57:39 UTC+0100 From: Reinaldo Pis Diez Subject: Symmetry label for molecular states To: chemistry@ccl.net Message-id: <350*/RFC-822=pis(u)diez(a)cpd.uva.es/OU=cpd/O=uva/PRMD=iris/ADMD=mensatex/C=es/@MHS> Content-identifier: 350 Content-transfer-encoding: 7BIT Conversion: Prohibited Importance: high Priority: urgent X400-Content-type: P2-1984 (2) X400-MTS-identifier: [/PRMD=iris/ADMD=mensatex/C=es/;940223115739] X400-Originator: pis_diez@cpd.uva.es X400-Recipients: chemistry@ccl.net Hi all netters! This is perhaps a very naive question but I wasn't be able to find the appropriate bibliography. My problem is as follows: I've got an open-shell mole- cule belonging to Td symmetry group. It has the configuration (1t_2)^2. The direct product t_2 x t_2 gives A_1 + E + T_1 + T_2. Now, is there any set of rules like Hund's ones for atomic configuration that allow one to decide which triplet is the most stable, 3A_1, 3E, 3T_1 or 3T_2? Any answer or book reference is welcome ( I tried the Herzberg's and some books on Quantum Chemistry but the info isn't com- plete). Please send mails to me. Thanks in advance, Reinaldo