From laaksone@csc.fi Wed Apr 1 00:21:33 1998 Received: from pobox.csc.fi for laaksone@csc.fi by www.ccl.net (8.8.3/950822.1) id AAA20899; Wed, 1 Apr 1998 00:00:17 -0500 (EST) Received: from laaksonen.csc.fi (laaksonen.csc.fi [193.166.1.75]) by pobox.csc.fi (8.8.8/8.8.8/CSC/Rtrs-1.13) with SMTP id IAA29974 for ; Wed, 1 Apr 1998 08:00:16 +0300 (EET DST) Date: Wed, 1 Apr 1998 07:57:20 +0300 (GFT Daylight Time) From: Leif Laaksonen To: chemistry@www.ccl.net Subject: Linux version of gOpenMol revisited Message-ID: X-X-Sender: laaksone@laaksonen.csc.fi MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL members, The yesterday announced Linux version of gOpenMol was linked with a dynamic Motif library. Most of you don't have Motif so I remade the program using static libraries. I apologize for the fuss. Please feel free to reload the new version from: http://laaksonen.csc.fi/gopenmol/ Regards, -leif laaksonen ------------------------------------------------------------------- Center for Scientific Computing | Phone: 358 9 4572378 P.O. Box 405 | Mobile: 358 400425203 FIN-02101 Espoo | Telefax: 358 9 4572302 FINLAND | Mail: Leif.Laaksonen@csc.fi -------- URL: http://laaksonen.csc.fi/leif.laaksonen.html --------- From jkl@ccl.net Wed Apr 1 02:21:35 1998 Received: from ccl.net for jkl@ccl.net by www.ccl.net (8.8.3/950822.1) id BAA21900; Wed, 1 Apr 1998 01:46:08 -0500 (EST) Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id BAA17528; Wed, 1 Apr 1998 01:46:06 -0500 (EST) From: Jan Labanowski Received: for jkl@ccl.net by krakow.ccl.net (8.8.3/920428.1525) id BAA29316; Wed, 1 Apr 1998 01:46:06 -0500 (EST) Date: Wed, 1 Apr 1998 01:46:06 -0500 (EST) Message-Id: <199804010646.BAA29316@krakow.ccl.net> To: chemistry@www.ccl.net Subject: Symposium: Ohio Molecular Computation and Simulation Network, Apr 17, 1998 Forwarding: Mail from 'jfried@alpha.che.uc.edu (Joel R. Fried)' dated: Mon, 30 Mar 1998 13:18:40 -0500 (EST) Cc: jkl@ccl.net 1st Annual Symposium Ohio Molecular Computation and Simulation Network Friday, April 17, 1998 Cincinnati, Ohio The program and registration information for the First Annual Symposium of the Ohio Molecular Computation and Simulation Network is posted at our Web Site at http://www.obr-camd.che.uc.edu/ Jan Labanowski jkl@ccl.net From jolanala@main.amu.edu.pl Wed Apr 1 02:29:58 1998 Received: from main.amu.edu.pl for jolanala@main.amu.edu.pl by www.ccl.net (8.8.3/950822.1) id BAA21942; Wed, 1 Apr 1998 01:49:36 -0500 (EST) From: Received: from ppp (pppa199.poznan.tpnet.pl [194.204.178.199]) by main.amu.edu.pl (8.8.8/8.8.8) with SMTP id IAA31931 for ; Wed, 1 Apr 1998 08:49:23 +0200 (MET DST) Message-Id: <199804010649.IAA31931@main.amu.edu.pl> Comments: Authenticated sender is To: CHEMISTRY@www.ccl.net Date: Wed, 1 Apr 1998 08:48:00 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: impact factors - summary X-Confirm-Reading-To: jolanala@main.amu.edu.pl X-pmrqc: 1 Return-receipt-to: jolanala@main.amu.edu.pl Priority: urgent X-mailer: Pegasus Mail for Win32 (v2.54) Dear all, Yesterday, I asked about impact factors. Bellow, you will find a summary. Thank you very much for help, Jolanta ********************************************************** Hellow, For impact factors of 1994, see: http://biophysik.uni-goettingen.de/Biophysik_HomePage/SCI.html For impact factors of 1995, see: http://www.unizh.ch/onkwww/journal2.html#P Best wishes, Luis Salvatella _______ From Ralph Merkle: The journal Nanotechnology had a 1996 impact factor of 1.881, which placed it at the top of its category in engineering. (see: http://www.ioppublishing.com/Journals/Catalogue/NA) This is remarkably good for a new journal. Phys Rev A (listed in the URL given below) had a 1992 impact factor of 2.157 Impact factors for some physics journals are given at: http://arcadia.tuniv.szczecin.pl/impact.html A brief discussion of the impact factor, along with links to two articles on the subject, is at http://www.isinet.com/guidebk/glossary.html#impact factor ______________ Here is a table with the Impact Factors(IF) of year 1996 (Source: Institute of Scientific Information, Philadelphia) Copied from CHEMISTRY, A Europian Journal 1998, 4/1 Editorial Journal IF ----------------- --------------- Chem. Rev. 17.112 Acc. Chem. Res. 10.646 Angew. Chem. Int.(Eng) 8.184 Chem. Soc. Rev. 6.223 J. Am. Chem. Soc. 5.948 Chem. Eur. J. 4.814 Anal. Chem. 4.550 J. Med. Chem 4.453 J. Org. Chem. 3.722 Adv. Mater. 3.630 J. Chem Phys. 3.520 J. Phy. Chem 3.370 Organometallics 3.134 J. Chem. Soc. Chem Comm. 3.107 Inorg. Chem 2.990 Tetrahedron Lett. 2.497 Helv. Chim. Acta. 2.369 Tetrahedron 2.232 J. Chem. Soc. Dalton Trans. 2.200 Chem. Ber. 1.958 New. J. Chem. 1.813 J. Chem Soc. Perkin trans.I 1.799 J. Organomet. Chem. 1.794 Chem. Lett. 1.631 Leibigs Ann. 1.549 Z. Anorg. Allg. Chem 1.159 J. Prakt. Chem. 0.551 Pol. J. Chem. 0.492 ---------------------------------------------------------- Cheers, Jamal Uddin AK Frenking Philipps-Universitaet Marburg Fachbereich Chemie D-35032, Germany ________________ check out the following link for journal impact factors: http://www.med-rz.uni-sb.de/ubuklu/impact2.html Best regards, Thomas ( @ - ) ------------------oOOo----(_)----oOOo------------------ Thomas Hermann Institut de Biologie Moleculaire et Cellulaire (IBMC) UPR9002 du CNRS 15 rue Rene Descartes F-67084 Strasbourg Cedex Tel. +(33) 3.88.41.70.49 France Fax +(33) 3.88.60.22.18 ------------------------------------------------------- Which Journals do you want? Some of them is listed below:(from JCR 1996) Angew Chem Int Ed 8.184 J Am Chem Soc 5.948 Chem-Eur J 4.814 J Chem Phys 3.516 J Phys Chem-US 3.366 Chem Phys Lett 2.589 Helv Chim Acta 2.369 J Chem Soc Faraday T 1.663 Chiu Wing Lok Abe Kurtz Nuclear Magnetic Resonance Group Dept. of Chem. CUHK E-mail :kurtz@iris.chem.cuhk.edu.hk Phone :(852) 2609 6317 Fax :(852) 2603 5057 Address: LG54, Science Centre, Department of Chemistry, Chinese University of Hong Kong Hong Kong From bruno@antas.agraria.uniss.it Wed Apr 1 03:21:35 1998 Received: from cinymp.cineca.it for bruno@antas.agraria.uniss.it by www.ccl.net (8.8.3/950822.1) id CAA22425; Wed, 1 Apr 1998 02:49:50 -0500 (EST) Received: from antas.agraria.uniss.it by cinymp.cineca.it (5.61/UNICOS-PP) id AA66126; Wed, 1 Apr 98 09:50:00 +0200 Date: Wed, 1 Apr 1998 08:47:38 +0100 (NFT) From: "Dr. Bruno Manunza" To: Eva Young Cc: ccl Subject: Re: CCL:pdb to VRML conversion tool In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 31 Mar 1998, Eva Young wrote: > Hi folks: > > Is there an authoring tool available that will convert pdb files to VRML? > > I'll summarize any replies to the list. > > Eva > > Eva Young > University of Minnesota > eyoung@biosci.umn.edu > Dear Eva, have a look at: http://ws05.pc.chemie.th-darmstadt.de/vrml/pdb2vrml.html regards Bruno Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it web: http://antas.agraria.uniss.it From ric@ws0e.pc.chemie.tu-darmstadt.de Wed Apr 1 03:37:59 1998 Received: from ws0e.pc.chemie.tu-darmstadt.de for ric@ws0e.pc.chemie.tu-darmstadt.de by www.ccl.net (8.8.3/950822.1) id CAA22296; Wed, 1 Apr 1998 02:27:11 -0500 (EST) Received: (from ric@localhost) by ws0e.pc.chemie.tu-darmstadt.de (950413.SGI.8.6.12/950213.SGI.AUTOCF) id JAA06446; Wed, 1 Apr 1998 09:27:02 +0200 From: ric@ws0e.pc.chemie.tu-darmstadt.de (Richard Marhoefer) Message-Id: <9804010927.ZM6444@ws0e.pc.chemie.tu-darmstadt.de> Date: Wed, 1 Apr 1998 09:27:01 -0500 In-Reply-To: Eva Young "CCL:pdb to VRML conversion tool" (Mar 31, 17:41) References: X-Face: #w@@!I[Lf"(:7]}[`Dp6S:Opmr.r[%;@v9L3Rim7zL4Iw?tQ~ntPtj|'23!-t;2)^ZI;Sg^tb,QOwfcuG~T0d,/TaHq,=DA2+|A?%|,ChO^m' X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: Eva Young , ccl Subject: Re: pdb to VRML conversion tool Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Mar 31, 17:41, Eva Young wrote: > Subject: CCL:pdb to VRML conversion tool >> Hi folks: >> >> Is there an authoring tool available that will convert pdb files to VRML? >> >> I'll summarize any replies to the list. >> Hi, you can find our pdb2vrml converter under the following URL: http://www.pc.chemie.tu-darmstadt.de/vrml/pdb2vrml.html Richard -- Dipl.-Ing. Richard J. Marhoefer Technische Universitaet Darmstadt Physikalische Chemie I, Petersenstr. 20, 64287 Darmstadt fon: (+int49) 6151/16-3746 fax: (+int49) 6151/16-4298 mail: ric@pc.chemie.tu-darmstadt.de net: http://www.pc.chemie.tu-darmstadt.de/authors/ric/ -------Please note our new e-mail / s-mail address------- From N.Goldberg@tu-bs.de Wed Apr 1 04:21:36 1998 Received: from rzcomm1.rz.tu-bs.de for N.Goldberg@tu-bs.de by www.ccl.net (8.8.3/950822.1) id DAA22550; Wed, 1 Apr 1998 03:35:12 -0500 (EST) Received: from tu-bs.de (bonding.org-chem.nat.tu-bs.de [134.169.19.161]) by rzcomm1.rz.tu-bs.de (8.8.6/8.8.6) with ESMTP id KAA12683 for ; Wed, 1 Apr 1998 10:34:45 +0200 (METDST) Message-ID: <3521FC2C.2754649C@tu-bs.de> Date: Wed, 01 Apr 1998 10:34:52 +0200 From: Norman Goldberg X-Mailer: Mozilla 4.03 [de] (Win95; I) MIME-Version: 1.0 To: "CHEMISTRY@www.ccl.net" Subject: descriptors for the 'shape' and 'size' of molecules Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, I am looking for a simple (!?) method to describe the 'size' and topology of a molecule. The aim is to establish a correlation between experimentally observed retention times (by liquid cromatography) and the 'shape' of several pure hydrocarbons (bigger species including 'disk' and umbrella-shaped molecules). I have no experience in this field of research, whatsoever, so any hints or comments would be appreciated. Many thanks in advance, Norman -- _____________________________________ Dr. Norman Goldberg (N.Goldberg@tu-bs.de) Technische Universitaet Braunschweig Institut fuer Organische Chemie Hagenring 30 D-38106 Braunschweig (FRG) Tel.: +(0)531-391-5312 Fax : +(0)531-391-5388 http://www.tu-bs.de/institute/org-chem/goldberg/WELCOME.htm From aguado@jmlopez.fam.cie.uva.es Wed Apr 1 05:21:38 1998 Received: from jmlopez.fam.cie.uva.es for aguado@jmlopez.fam.cie.uva.es by www.ccl.net (8.8.3/950822.1) id EAA22869; Wed, 1 Apr 1998 04:36:27 -0500 (EST) Received: (from aguado@localhost) by jmlopez.fam.cie.uva.es (8.8.3/8.8.3) id LAA01603 for chemistry@www.ccl.net; Wed, 1 Apr 1998 11:41:50 +0200 Date: Wed, 1 Apr 1998 11:41:50 +0200 From: Andres Aguado Message-Id: <199804010941.LAA01603@jmlopez.fam.cie.uva.es> To: chemistry@www.ccl.net Subject: Pair potentials for metal oxides... Dear Netters: A week ago I posted a question concerning the simulation of oxides using pair potentials. I wish to thank Manuel, Claudio, and Dewi for kindly responding. Their answers were the same. Anyone interested in this item should take a look to the following references and web direction: .......................................................................... TI: SELF-CONSISTENT INTERATOMIC POTENTIALS FOR THE SIMULATION OF BINARY AND TERNARY OXIDES AU: BUSH_TS, GALE_JD, CATLOW_CRA, BATTLE_PD JN: JOURNAL OF MATERIALS CHEMISTRY, 1994, Vol.4, No.11, p.1765 TI: SELF-CONSISTENT INTERATOMIC POTENTIALS FOR THE SIMULATION OF BINARY AND TERNARY OXIDES AU: BUSH_TS, GALE_JD, CATLOW_CRA, BATTLE_PD JN: JOURNAL OF MATERIALS CHEMISTRY, 1994, Vol.4, No.6, pp.831-837 http://www.ch.ic.ac.uk/gale/Research/gulp.html#Potentials ........................................................................... Best regards, Andres Aguado aguado@jmlopez.fam.cie.uva.es http://jmlopez.fam.cie.uva.es/~aguado From jaouad@csc.fi Wed Apr 1 07:21:36 1998 Received: from pobox.csc.fi for jaouad@csc.fi by www.ccl.net (8.8.3/950822.1) id GAA23345; Wed, 1 Apr 1998 06:39:23 -0500 (EST) Received: from cypress.csc.fi (cypress-e.csc.fi [128.214.46.7]) by pobox.csc.fi (8.8.8/8.8.8/CSC/Rtrs-1.13) with SMTP id OAA12159 for ; Wed, 1 Apr 1998 14:39:22 +0300 (EET DST) Date: Wed, 1 Apr 1998 14:39:21 +0300 (EET DST) From: Jaouad El-Bahraoui Reply-To: Jaouad El-Bahraoui To: CHEMISTRY@www.ccl.net Subject: Inorganic and organometalic chemistry Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi!!! my particular interest is the prediction of the electronic coupling between the cluster ligand and the resulting redox properties. I have no experience in this field of research, so any hints or comments would be appreciated. Many thanks in advance, \^ ^/ )@ @( +-----------------------oOO--(_)----------------------------------+ | Jaouad El-Bahraoui , Ph.D | +-----------------------------------------------------------------+ | Inorganic Chemistry Laboratory | Tel: +358-9-19140199 | | department of Chemistry, P.O. BOX 55 | Fax: +358-9-19140198 | | University of Helsinki,FIN-00040 | jaouad@ccsc.fi | | Helsinki, Finland |http://w3.ugr.es/~jaouad/| +----------------------Oooo--oOO----------------------------------+ oooO ( ) ( ) ) / \ ( (_/ \_) -------------------------------------------------------------------- I know you believe you understand what you think I said, but I am not sure you realize that what you heard is not what I meant. -------------------------------------------------------------------- From darrena@chem.leeds.ac.uk Wed Apr 1 11:21:39 1998 Received: from chemistry.leeds.ac.uk for darrena@chem.leeds.ac.uk by www.ccl.net (8.8.3/950822.1) id KAA24843; Wed, 1 Apr 1998 10:46:49 -0500 (EST) Received: from [129.11.12.138] (chmmac37.leeds.ac.uk [129.11.12.138]) by chemistry.leeds.ac.uk (8.8.8/8.8.8) with ESMTP id QAA19916 for ; Wed, 1 Apr 1998 16:46:24 +0100 (BST) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 1 Apr 1998 16:44:43 +0100 To: chemistry@www.ccl.net From: Darren Andrews Subject: Compiling CADPAC6 under Linux I am trying to compile CADPAC6 under Red Hat 5.0 Linux on a Pentium II. Has anybody done this with the usual fortran compilers? I just get loads of compiler errors, presumably because the makefile is all wrong. Cheers, Darren Andrews. PostGraduate Student, School of Chemistry, University of Leeds, Leeds. LS2 9JT. England. Darrena@chem.leeds.ac.uk Tel: 0113 233 6594. Fax: 0113 233 6565. From mn1@helix.nih.gov Wed Apr 1 11:27:54 1998 Received: from helix.nih.gov for mn1@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id KAA24619; Wed, 1 Apr 1998 10:25:06 -0500 (EST) Received: (from mn1@localhost) by helix.nih.gov (8.8.5/8.8.5) id KAA15694; Wed, 1 Apr 1998 10:25:02 -0500 (EST) Date: Wed, 1 Apr 1998 10:25:02 -0500 (EST) From: "M. Nicklaus" Message-Id: <199804011525.KAA15694@helix.nih.gov> To: CHEMISTRY@www.ccl.net Subject: SUMMARY: MB (or MW) in Gaussian 94 Cc: mn1@helix.nih.gov Hi, I asked the following QUESTION ======== > How does G94 count one MB (or MW) in the %Mem command? > Is it 1 x (or 8 x) 1,000,000; > or 1 x (or 8 x) 2^20 = 1 x (or 8 x) 1,048,576 ? > > Hence, do the commands > %Mem=8000000 > %Mem=8MW > %Mem=64MB > all mean exactly 64,000,000 or 67,108,864 bytes? > > I tend toward the first interpretation, but since the > manual does not seem to spell this problem out explicitly, > I thought I'd ask... If we go with Doug Fox's answer, then the Gaussian 94 User's Reference is wrong. On p. 10, it states: "For example, the following command sets memory use to 64 MB: %Mem=8000000 [... T]he following command also sets the amount of dynamic memory to 64 MB: %Mem=64M" Can this be confirmed? Here are the RESPONSES ========= Brian Salter-Duke 8000000 means 8MW or 64,000,000 bytes. I tend to avoid using anything in this command other than in words. MW may not work correctly. It certainly does not in the %rwf line. --------- Rick Venable Your real question is the meaning of MEGA in these contexts; certainly 64MB has to be 64*1024*1024 by definition, but it's less clear for a megaword, although one would hope for consistency. My guess is that 8MW == 64MB, but not 8000000 words. You should be able to test this empirically, I would think. --------- gaussian.com!fox@lorentzian.com (Doug Fox) MB and MW are powers of 2 not decimal numbers so 8000000 is not identical with 8MW or 64MB. The latter two are identical and have the value of 6710864. [I guess you meant 67108864. M.N.] ------------------------------------------------------------------------ Marc ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 37, Rm 5B29 Phone: (301) 402-3111 37 Convent Dr, MSC 4255 Fax: (301) 496-5839 BETHESDA, MD 20892-4255 USA http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm Laboratory of Medicinal Chemistry, National Cancer Institute, & Center for Molecular Modeling, Div. of Computer Research and Technology ------------------------------------------------------------------------ From fparnold@balihai.uchicago.edu Wed Apr 1 13:21:40 1998 Received: from balihai.uchicago.edu for fparnold@balihai.uchicago.edu by www.ccl.net (8.8.3/950822.1) id NAA25653; Wed, 1 Apr 1998 13:07:55 -0500 (EST) Received: from localhost by balihai.uchicago.edu via SMTP (950413.SGI.8.6.12/931108.SGI.ANONFTP) for id MAA05965; Wed, 1 Apr 1998 12:07:52 -0600 Date: Wed, 1 Apr 1998 12:07:52 -0600 (CST) From: "Fred P. Arnold" To: Computational Chemistry List Subject: Contracting a Basis Set. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello: I hate to admit my total lack of clue in this instance, but does anyone have a suggestion as to how to efficiently (or correctly) contract a basis set, i.e. how do I optimize the coefficients? I want to use the CRENBL ECP and associated basis set from the EMSL collection, but doubt that a formally core orbital (5d on Thallium) needs to be quadruple-zeta. I would like to contract this to double zeta at worst, and then leave the valence s-p as uncontracted triple zeta. Thank you for your time. -Fred "Contrary to popular belief, most C++ Frederick P. Arnold, Jr. programs are not written by disorganized Advanced Research Systems orangutans using Zen programming techniques 5640 S. Ellis Ave and poorly commented in Esperanto..." S. Oualline Chicago, IL 60637 From qiang@tammy.harvard.edu Wed Apr 1 14:21:40 1998 Received: from tammy.harvard.edu for qiang@tammy.harvard.edu by www.ccl.net (8.8.3/950822.1) id NAA25834; Wed, 1 Apr 1998 13:23:42 -0500 (EST) Received: from tammy.harvard.edu (nas5-31.fas.harvard.edu [140.247.45.131]) by tammy.harvard.edu (8.8.2/8.8.2) with ESMTP id NAA25696; Wed, 1 Apr 1998 13:31:37 -0500 (EST) Message-ID: <352287BC.DF448B91@tammy.harvard.edu> Date: Wed, 01 Apr 1998 13:30:20 -0500 From: "Qiang, Cui" X-Mailer: Mozilla 4.04 [en] (Win95; I) MIME-Version: 1.0 To: Norman Goldberg CC: "CHEMISTRY@www.ccl.net" Subject: Re: CCL:descriptors for the 'shape' and 'size' of molecules References: <3521FC2C.2754649C@tu-bs.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Norman Goldberg wrote: > Hello, > > I am looking for a simple (!?) method to describe the 'size' and > topology of a molecule. > The aim is to establish a correlation between experimentally observed > retention times (by liquid cromatography) and the 'shape' of several > pure hydrocarbons > (bigger species including 'disk' and umbrella-shaped molecules). > As a matter of fact, the issue is rather similar to some of the drug design problem, just that the observable is kind of different. But u can certainly borrow some technique such as GA-NN (genetic algorithm-neural network) to set up the correlation. Look at some standard book on NN, and some paper on 2D/3D drug-design ( for instance, I recommand several paper by S. So and M. Karplus, published in J. Med. Chem.; for more info, see http://yuri.harvard.edu/~so) Good luck! > I have no experience in this field of research, whatsoever, so any hints > or comments > would be appreciated. > > Many thanks in advance, > > Norman > > -- > _____________________________________ > > Dr. Norman Goldberg (N.Goldberg@tu-bs.de) > Technische Universitaet Braunschweig > Institut fuer Organische Chemie > Hagenring 30 > D-38106 Braunschweig (FRG) > > Tel.: +(0)531-391-5312 > Fax : +(0)531-391-5388 > > http://www.tu-bs.de/institute/org-chem/goldberg/WELCOME.htm > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: N.Goldberg@tu-bs.de > -- Original Sender From: Address: N.Goldberg@tu-bs.de > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html From ci_parkinson@pnl.gov Wed Apr 1 19:21:42 1998 Received: from pnl.gov for ci_parkinson@pnl.gov by www.ccl.net (8.8.3/950822.1) id TAA28622; Wed, 1 Apr 1998 19:01:07 -0500 (EST) Received: from pnl.gov (scoobie.emsl.pnl.gov) by pnl.gov (PMDF V5.1-10 #21283) with ESMTP id <01IVCZXI9VGW8X65KF@pnl.gov> for chemistry@www.ccl.net; Wed, 1 Apr 1998 16:01:01 PST Date: Wed, 01 Apr 1998 16:01:30 -0700 From: Chris Parkinson Subject: The EMSL Publisher - Demonstration Available To: chemistry@www.ccl.net Message-id: <3522C747.659C2E04@pnl.gov> MIME-version: 1.0 X-Mailer: Mozilla 4.04 (Macintosh; I; PPC) Content-type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-transfer-encoding: 7bit The EMSL Publisher (Lite) - Demonstration version now available http://www.emsl.pnl.gov:2080/proj/publisher/publisher.html The EMSL Publisher (c) 1997-1998 is a new software product developed to aid the process of writing scientific reports and journal articles. This document processing application is written entirely using the Java1.1 language, and as such will run on all supporting platforms (currently including Win95, WinNT, MacOS, and many UNIX flavors). In addition to offering the user the standard word processing features, the software also offers : * Embeddable Java Applets and JavaBeans This allows any Java code to be embedded within the document, code such as molecular editors, graphs, charts, equations etc... The demonstration version includes an example 3D Molecular Viewer, which allows 'live' 3D models to be placed into the document. * Distributed Document Server The user has the option to save and load his document to and from either the local disk or to a remote document server. This enables multiple authors to jointly write papers even if they are physically separate form each other and/or using different platforms. * Citations Database Built into the full release version of the software is a complete citations database, allowing references to be placed within documents, and then automatically formatted and numbered as required. * Automatic Journal Styling Papers can be written and then automatically styled for the destination journal. i.e., style for an JACS submission, and then with one click, re-style the whole document (references includes) for a J. Chem. Soc. submission. * Platform Independence The Publisher itself will run on any Java1.1 enabled machine. In addition, its documents are fully portable. * Chemical Formulae Styling Type in a chemical formula in plain text, have the software automatically superscript or subscript the numbers, and place 'proper' arrows where needed. We have just released a demonstration version of the Publisher Lite, showcasing the basic features of the software, and are anticipating a full featured release during the forthcoming summer. We'd be grateful if you would take a look at the web site, which details the project, download and test the software and pass on your valuable comments and suggestions. web : www.emsl.pnl.gov:2080/proj/publisher/publisher.html email : publisher@emsl.pnl.gov The Environmental Molecular Sciences Laboratory is a Scientific User Facility at Pacific Northwest National Laboratory funded by the Office of Biological and Environmental Research in the U.S. Department of Energy. PNNL is operated by Battelle Memorial Institute for DOE under contract DE-AC06-76RLO 1830. From m.dooley@mailbox.uq.edu.au Wed Apr 1 21:21:43 1998 Received: from bunyip.cc.uq.edu.au for m.dooley@mailbox.uq.edu.au by www.ccl.net (8.8.3/950822.1) id UAA29337; Wed, 1 Apr 1998 20:38:22 -0500 (EST) Received: from peta.ddd.uq.oz.au (peta.ddd.uq.edu.au [130.102.118.65]) by bunyip.cc.uq.edu.au (8.8.7/8.8.8) with SMTP id LAA03781 for <@bunyip.cc.uq.oz.au:chemistry@www.ccl.net>; Thu, 2 Apr 1998 11:38:20 +1000 Received: from extreme.ddd.uq.oz.au by peta.ddd.uq.oz.au via ESMTP (951211.SGI.8.6.12.PATCH1042/951211.SGI) for <@peta.ddd.uq.oz.au:chemistry@www.ccl.net> id LAA15815; Thu, 2 Apr 1998 11:38:40 -1000 Received: from chico.ddd.uq.oz.au by extreme.ddd.uq.oz.au via ESMTP (951211.SGI.8.6.12.PATCH1502/951211.SGI) for <@extreme.ddd.uq.oz.au:chemistry@www.ccl.net> id LAA29424; Thu, 2 Apr 1998 11:38:38 -1000 Received: from chico.ddd.uq.oz.au by chico.ddd.uq.oz.au via SMTP (951211.SGI.8.6.12.PATCH1042/940406.SGI.AUTO) for id LAA01554; Thu, 2 Apr 1998 11:38:36 -1000 Sender: dooley@mailbox.uq.edu.au Message-ID: <3524055B.167E@mailbox.uq.edu.au> Date: Thu, 02 Apr 1998 11:38:35 -1000 From: Michael Dooley X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP20) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: macromodel and GRASP questions Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello CCLer's, macromodel question: I'm optimising a batchmin com file at the moment that does a monte carlo conformational search. The structures I'm looking at are peptides, so I would like to use a torsion selection function to favor random torsion angles near to the trans and cis minima of the peptide bonds. Is there a way to set up the opcode MCTS to do this? Or some other way? GRASP question: Having some problems with display of dipole moments. I read in a pdb file and set full crg, calculate and display the dipole moment... no problems. I repeat this on the second pdb file... no problems, but when I read in the third pdb file and calculate the dipole moment, the first protein's dipole moment shifts. I haven't tried reading in a fourth pdb file and calcuating the d.m. to see what happens. What I'm trying to do is compare the dipole moment of a group of overlayed structures. I'm not sure what's going on! In addition, I have a small peptide for which I calculated and displayed a dipole moment. I then mutated all of the positively charged residues on one face of the peptide (3 in all) to glutamate residues to create a mutant peptide, and calculated the dipole for this molecule (rereading the full.crg file). It superimposed PERFECTLY with the dipole of the unmutated molecule. Intuitively, this seemed odd. Am I doing something wrong? Can someone suggest another program that calculates and displays dipole moments of peptides and proteins? Cheers Michael -- Michael Dooley PhD Centre for Drug Design and Development The University of Queensland Brisbane Qld 4072 Australia m.dooley@mailbox.uq.edu.au From shenkin@still3.chem.columbia.edu Wed Apr 1 23:21:44 1998 Received: from mailrelay1.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.8.3/950822.1) id XAA29947; Wed, 1 Apr 1998 23:17:07 -0500 (EST) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id XAA27980; Wed, 1 Apr 1998 23:15:32 -0500 (EST) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) id XAA28214; Wed, 1 Apr 1998 23:15:31 -0500 Date: Wed, 1 Apr 1998 23:15:31 -0500 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <199804020415.XAA28214@still3.chem.columbia.edu> To: chemistry@www.ccl.net, Michael Dooley Subject: Re: CCL:macromodel and GRASP questions > From chemistry-request@www.ccl.net Wed Apr 1 22:07:50 1998 > Subject: CCL:macromodel and GRASP questions > macromodel question: I'm optimising a batchmin com file at the moment > that does a monte carlo conformational search. The structures I'm > looking at are peptides, so I would like to use a torsion selection > function to favor random torsion angles near to the trans and cis minima > of the peptide bonds. Is there a way to set up the opcode MCTS to do > this? Or some other way? I can help with this one. First, as the manual implies, MCTS has not proved to be a terribly useful facility. If you are actually sampling the peptide bonds, a good optimization is to set args5=90 and arg6=180; this will pretty much guarantee that any time you try to alter a peptide bond, you'll flip it, and you can't get more efficient than that at overcoming barriers. (Args 5 & 6 set the minimum and maximum absolute values of a change to the bond; actually, a random number is thrown between these two values if the bond is altered in a trial.) Recall that every trial conformation is minimized, so fitting the torsional trials to the local potential about the bond, as MCTS tries to do, might save a little minimization time, but that's all it will do. However, please note that if you set up a csearch from the GUI, peptide bonds will not be sampled by default; quite the opposite: they will be frozen into their starting conformations with TORC commands. So you should be sure that you don't have TORC commands present for any peptide bonds you want to sample. Slight clarification: "frozen" in the last paragraph is too strong a term. TORC (TORsional Constraint) actually rules out any structure for which the listed bond is not within the limits given in the command; so if a peptide bond starts out trans, a TORC command would ordinary be put in to reject any structure in which it winds up cis. Obviously, you don't want this if you wish to allow this transition to take place. -P. ************** In memoriam, Grandpa Jones, 1913-1998, R.I.P. ************** * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html *