From pkw@iglou.com Wed Feb 1 02:41:29 1995 Received: from relay4.UU.NET for pkw@iglou.com by www.ccl.net (8.6.9/930601.1506) id BAA11438; Wed, 1 Feb 1995 01:47:42 -0500 Received: from iglou.iglou.com by relay4.UU.NET with SMTP id QQybdz21861; Wed, 1 Feb 1995 01:47:41 -0500 Received: by iglou.iglou.com (Smail3.1.28.1 #2) id m0rZYpa-0001yMC; Wed, 1 Feb 95 01:46 EST Date: Wed, 1 Feb 1995 01:46:22 -0500 (EST) From: Paul Kevin Wilson X-Sender: pkw@iglou To: CHEMISTRY@ccl.net Subject: Fission in a flask Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Has anyone subscribing to this forum heard of any research on affecting the spontaneous fission rate of one of the heavy elements through chemical reactions. As I understand, it is theoretically possible but the problem in reality lies with how slow chemical reactions are relative to the dynamics of the nucleus. From kris@bionmr1.rug.ac.be Wed Feb 1 03:41:26 1995 Received: from mserv.rug.ac.be for kris@bionmr1.rug.ac.be by www.ccl.net (8.6.9/930601.1506) id DAA12392; Wed, 1 Feb 1995 03:10:53 -0500 Received: from bionmr1.rug.ac.be by mserv.rug.ac.be with SMTP id AA18232 (5.67b/IDA-1.5 for <@mserv.rug.ac.be:chemistry@ccl.net>); Wed, 1 Feb 1995 09:09:56 +0100 Received: by bionmr1.rug.ac.be (940715.SGI.52/931108.SGI.AUTO.ANONFTP) for @mserv.rug.ac.be:chemistry@ccl.net id AA13260; Wed, 1 Feb 95 09:05:52 +0100 From: "Kris Boulez" Message-Id: <9502010905.ZM13258@bionmr1.rug.ac.be> Date: Wed, 1 Feb 1995 09:05:49 +0100 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: WWW pages on chemical mailing lists Cc: Kris.Boulez@rug.ac.be Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Hello, Based on raw data from Jan Labanowski (jkl@ccl.net) I composed a set of WWW pages on chemistry related mailing lists. For each list there is a short description, the name of the editor, the subscription address, the location of the archives. These pages can be found at http://bionmr1.rug.ac.be/chemistry/overview.html Jan Labanowski and I agreed that I'll keep this list up-to-date. So if there any additions, corrections, remarks mail them to me (Kris.Boulez@rug.ac.be). Kris, -- Kris Boulez (Kris.Boulez@rug.ac.be) Biomolecular NMR unit University of Ghent, Belgium From kamal@univ-orleans.fr Wed Feb 1 06:41:27 1995 Received: from centre.univ-orleans.fr for kamal@univ-orleans.fr by www.ccl.net (8.6.9/930601.1506) id GAA12941; Wed, 1 Feb 1995 06:10:02 -0500 Received: from mailhost.univ-orleans.fr ([193.49.81.2]) by centre.univ-orleans.fr (8.6.9/8.6.9) with SMTP id MAA05084 for ; Wed, 1 Feb 1995 12:02:21 +0100 LD?Resent-Date: Wed, 1 Feb 1995 12:02:21 +0100 Message-Id: <199502011102.MAA05084@centre.univ-orleans.fr> X-Sender: kamal@mailhost.univ-orleans.fr X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 01 Feb 1995 11:56:14 +0000 To: chemistry@ccl.net From: kamal@univ-orleans.fr (Kamal Azzaoui) Subject: pi-pi interactions block Hello Netters I summarized here all the answers about my question : > Does anybody can help me to get references about pi-pi interaction > > and how can determine it with computational chemistry (if possible) > > Any reponse will be appreciate > *************************************************************************** LD?Resent-Date: Tue, 31 Jan 1995 14:28:56 +0100 From: Magan Govender - PG To: kamal@univ-orleans.fr (Kamal Azzaoui) Date: Tue, 31 Jan 1995 15:22:12 +0200 (SAST) Subject: Re: CCL:pi-pi interactions X-pmrqc: 1 Priority: normal Dear Kamal, We are using a program based on Self Consistent THeory without any correlation effects, called Monstergauss. With the program one can break down the interaction energies into various components as to with dominant force holds the molecules together qualitatively. I am not sure whether it would suite your need. If you require a copy of this program I can email to you with some references. Regards ********************************************************************** LD?Resent-Date: Tue, 31 Jan 1995 14:47:20 +0100 From: MARTINN@UNCWIL.EDU Date: Tue, 31 Jan 1995 08:41:37 -0400 (EDT) Subject: Pi-Pi Interactions To: kamal@centre.univ-orleans.fr X-VMS-To: IN%"kamal@centre.univ-orleans.fr" Kamal, I, too, am interested in calculating pi-pi interactions, but I have not yet published anything. There was an article in J. Comp. Chem last August or so about Aryl-Aryl charge transfer complexes, but I do not have the reference at hand. I am doing similar calculations, but I have just started. Please summarize the (useful) replies and forward them to me. If I run across anything, I'll forward it to you. Ned Martin, Department of chemistry, University of North Carolina at Wilmington, Wilmington, NC (USA) 28403-3297 ************************************************************** LD?Resent-Date: Tue, 31 Jan 1995 15:17:59 +0100 From: Date: Tue, 31 Jan 1995 8:15:07 -0500 (EST) To: chemistry@ccl.net Subject: CCL:pi-pi interactions... Sender: Computational Chemistry List Errors-To: ccl@ccl.net Precedence: bulk > > ******************************************************************** Kamal, Take a look at: JACS, 1995, 117, 792. (most recent issue) Also: Hartsough, D. S., PhD Thesis, University of Illinois-Urbana Champaign, 1991 and references therein. Hope this helps, Jon --------------- Jon Erickson DowElanco Discovery jerickson@dowelanco.com -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: JERICKSON@ELINET1.DOWELANCO.COM -- Original Sender From: Address: JERICKSON@ELINET1.DOWELANCO.COM CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV ******************************************************************** LD?Resent-Date: Tue, 31 Jan 1995 16:31:52 +0100 From: "Erin Duffy" Date: Tue, 31 Jan 95 10:24:59 -0500 To: kamal@centre.univ-orleans.fr Subject: aryl-aryl interactions Hi - Check out the following: Jorgensen, W.L.; Severance, D.L. "Aromatic-Aromatic Interactions: Free Energy Profiles for the Benzene Dimer in Water, Chloroform, and Liquid Benzene." J. Am. Chem. Soc. (1990) v.112, 4768-4774. Ciao. - Erin (eduffy@laplace.csb.yale.edu) ******************************************************************** LD?Resent-Date: Tue, 31 Jan 1995 17:38:44 +0100 From: kit1000@cus.cam.ac.uk (Dr K.I. Trollope) Subject: Re: CCL:pi-pi interactions To: kamal@univ-orleans.fr (Kamal Azzaoui) Date: Tue, 31 Jan 1995 11:16:31 +0000 (GMT) Content-Length: 621 Try C.A. Hunter, J. Am. Chem. Soc., 112 (1990) 5525 This has been repeated with a newer force field, in J.G. Vinter, J. Computer-aided molecular design, 8 (1994) 653 Also, try P.W. Fowler, Biochem. Biophys. Res. Comm, 153 (1988) 1296 S.L. Price, J. Chem. Phys., 86 (5) 2859 --- Keith Trollope kit1000@cam.ac.uk Department of Chemistry +44 1223 336452 Lensfield Road Cambridge, UK ----------------------------------------------------------------------------- Bore, n. A person who talks when you want him to listen ******************************************************* LD?Resent-Date: Tue, 31 Jan 1995 19:17:07 +0100 To: Kamal Azzaoui From: Tim Mitchell-1 Date: 31 Jan 95 18:09:44 ES Subject: Re: CCL:pi-pi interactions Kamal -- Try looking at: CA Hunter J Chem Soc Chem Comm 1991 749-751 (pi-pi interactions in molecular recognition) S Paliwal S Greib and CS Wilcox JACS 1994 116 4497-4498 (measurement of edge-face pi pi interaactions) J Rebeck Angew Chem Int Ed Eng 1990 29 245-255 (measurement of face-face pi-pi interactions) GR Desiraju and KV Radha Kishan JACS 1989 111 4838-4843 (Stacked vs edge-face pi pi interactions) CA Hunter, J Singh and J Thornton J Mol Biol 1991 218 837-846 (Geometry of Phe-Phe interactions in proteins) I would be very grateful if you could send me a summary of any other replies you recieve Tim Mitchell, SmithKline Beecham, Brockham Park UK ********************************************************************** LD?Resent-Date: Tue, 31 Jan 1995 22:12:38 +0100 Date: Tue, 31 Jan 1995 16:14:23 -0500 From: "Siram N. V. Rao" To: kamal@centre.univ-orleans.fr Subject: Re: CCL:pi-pi interactions... Kamal: 1) JACS (1991), p. 5525, by: Hunters and Sanders 2) Current issue of J-CAMD ( journal of computer aided molecular design) has an article that deals with the application of this feature... Hope it helps. - rao email: rao@umdnj.edu ******************************************************************** Kamal AZZAOUI LCBA Universite d'Orleans France Tel 38-41-70-42 email : kamal@centre.univ-orleans.fr ******************************************************************** From mikes@bioch.ox.ac.uk Wed Feb 1 08:44:09 1995 Received: from oxmail.ox.ac.uk for mikes@bioch.ox.ac.uk by www.ccl.net (8.6.9/930601.1506) id HAA14024; Wed, 1 Feb 1995 07:47:28 -0500 From: Received: from opal.bioch.ox.ac.uk by oxmail.ox.ac.uk with SMTP (PP) id <23995-0@oxmail.ox.ac.uk>; Wed, 1 Feb 1995 09:42:59 +0000 Received: from ocms.ox.ac.uk (nmrpcd.ocms) by bioch.ox.ac.uk (5.0/SMI-SVR4) id AA07436; Wed, 1 Feb 1995 09:43:27 GMT Received: by ocms.ox.ac.uk (940816.SGI.8.6.9/bioch3.0) id JAA15383; Wed, 1 Feb 1995 09:43:25 GMT Date: Wed, 1 Feb 1995 09:43:25 GMT Message-Id: <199502010943.JAA15383@nmrpcd.ocms.ocms.ox.ac.uk> To: CHEMISTRY@ccl.net Subject: Public Domain Cluster Analysis Programs X-Mailer: [XMailTool v3.1.0] content-length: 512 Dear All, I am looking for a program to do simple cluster analysis given a (say) table of pairwise rmsds between structures. Can anyone tell me of useful programs to do this that exist in the public domain? Thanks Mike Smith --------------------------------------------------------------------- Mike Smith, | Phone: 01865 275981 Department of Biochemistry, | e-mail: mikes@bioch.ox.ac.uk Oxford University. | URL: http://nmra.ocms.ox.ac.uk/~mikes/ From peon@medchem.dfh.dk Wed Feb 1 09:09:15 1995 Received: from danpost.uni-c.dk for peon@medchem.dfh.dk by www.ccl.net (8.6.9/930601.1506) id HAA14082; Wed, 1 Feb 1995 07:54:40 -0500 Received: from medchem.dfh.dk (medchem.dfh.dk [129.142.148.31]) by danpost.uni-c.dk (8.6.4/8.6) with SMTP id NAA18984; Wed, 1 Feb 1995 13:50:14 +0100 Received: from [129.142.148.227] by medchem.dfh.dk via SMTP (920330.SGI/920502.SGI) for @danpost.uni-c.dk:HMARQUES@AURUM.CHEM.WITS.AC.ZA id AA07239; Wed, 1 Feb 95 12:49:23 +0100 Message-Id: <9502011149.AA07239@medchem.dfh.dk> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 1 Feb 1995 13:54:50 +0100 To: chemistry@ccl.net From: peon@medchem.dfh.dk (Per-Ola Norrby) Subject: Summary: Gas phase data Cc: carol@still3.chem.columbia.edu, garciae@ucsub.Colorado.EDU, WallyR@netcom.netcom.com, bcnlma@hkpu01.polyu.edu.hk, HMARQUES@AURUM.CHEM.WITS.AC.ZA Dear CCL:ers This may be a bit premature for a summary, but I have had some interesting responses. Many thanks to all who responded. ************************************************************************* Juergen Vogt wrote: >Our documentation group >has established a molecular physical and structural chemical database. Its >name is MOGADOC and deals with substances which were studied by microwave >spectroscopy, electron diffraction or molecular radio astronmy in the gas >phase. This comprehensive database has presently about 22000 bibliographic >entries for about 6000 compounds, inorganic, organic and organometallic >substances as well. It is distributed by FIZ Karlsruhe on diskette or CD-ROM. >Among our customers there some theoretical chemists. Moreover the last >update contains 3000 numerical datasets concerning bond distancies and angles. > >If you need more information please let me know. > > Yours sincerely > > Juergen Vogt > > Sektion fuer Spektren- > > und Strukturdokumentation > University of Ulm > D-89069 Ulm > Germany > > Tel. (+49) 731 4014-105 > Fax. (+49) 731 4014-117 The email address is: juergen.vogt@chemie.uni-ulm.de ************************************************************************* Another pointer to this database arrived from Ingo Steller: >A searcheable database for microwabe and electron diffraction data is >MOGADOC. It is a commercial program distributed in germany by >Fachinformationszentrum Karlsruhe, Germany. Also I think the >searchalgorithm is very bad (no structure search, only sum formulas), due >to the number of structures you can work with it. In the database you >will find all electron diffraction data from 1930 to now and all >microwave data from (I think) 1950 to now. >You can find a publication about the database in > >J. Vogt, Struct. Chem. 1992, Vol. 3, p ??? (I only have the masterprint) >Perhaps you can mail the author under the following address: > >vogt@rz.uni-ulm.d400.de ************************************************************************* Thomas R. Cundari wrote: > A good ref w/ numerous gas-phase data is the review by Hargittai. > >M. Hargittai, Coord. Chem. Rev., 91, 35 (1988). Gas Phase Structure of Metal >Halides. > >It is confined to metal halides and has a section on transition metal systems. > >I may be able to find individual references in our recent paper (M. T. Benson, >T. R. Cundari, S. J. Lim, H. D. Nguyen, K. Pierce-Beaver J. Am. Chem. Soc. >1994, 116, 3955 - 3966.) to work by individual groups by folks big in electron >diffraction of metal complexes, but I suspect they are well known to you >(Haaland, Page, etc.). > >Another ref I suspect you have seen is the book on multiply bonded complexes by >Nugent and Mayer. There is a complete chapter on structures (mostly X-ray but >some gas-phase ED structures) and one on vibrational data. [some deleted] ************************************************************************* Helder M. Marques wrote: >I don't know how many metal-containing structures there are in the >collection, but you might want to check Harmony et al, J Phys Chem >Ref Data, 8(3), 617, 1979. I'd be interested in seeing your summary. ************************************************************************* Per-Ola Norrby * Per-Ola Norrby * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk From usdccz73@ibmmail.com Wed Feb 1 09:41:36 1995 Received: from ibmmail.COM for usdccz73@ibmmail.com by www.ccl.net (8.6.9/930601.1506) id IAA15217; Wed, 1 Feb 1995 08:52:37 -0500 From: Message-Id: <199502011352.IAA15217@www.ccl.net> Received: from IBMMAIL.COM by ibmmail.COM (IBM VM SMTP V2R3) with BSMTP id 9025; Wed, 01 Feb 95 08:52:07 EST Date: Wed, 01 Feb 1995 08:52:01 EST To: chemistry@ccl.net, internet@ibmmail.com MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Subject: Pt parameter NOTE FROM: C. Qian usdccz73@ibmmail.com NITC EXPR CTR CO41B1 Tel. (517)496-6938, Fax (517)496-5121 SUBJECT: Pt parameter Dear all: Two weeks ago, I posted a question regarding the information of Platinum parameters and base set for Gaussian calculation. So far I got two responses ( I will summarize below). However, if you have any more suggestion, please send it to me or the net, thank you very much again. There are some Pt bases in Huzinaga's 'Green' Book: "Gaussian basis sets for molecular calculations", Physical science data Number 16, Pub: Elsevier 1984. John Waite (CHEM8@VAX.YORK.AC.UK) You of course know, that already in the G90 program there are some RECP and basis sets for Platinum. There are also other parameters awailable (Pseudopotentials Durand&Barthelat, Stoll&Preuss, Pitzer& Ermler, Christiansen etc.) The main problem is, that You have to intoduce both, the correlation and the ralativistic into Your calculaton in order to gain reasonable results. This may be a limiting factor according the system size. Due to the N**7 problem You will very fast run out of the disk/memory limits. Recently, we did MP2, CCSD(T) and DFT calculations on some M+(CnHm) systems (up to C6) and found the pertubational treatment suitable just for pure dative bonding. With platinum You have to take care about the nearly degenerated s1d9 and d10 states and MCSCF is strongly recommented. Anyway, I could try to find and send You few other references. However, try first with the Hay&Wadt RECP of gaussian Jan Hrusak C. Peter Qian NITC EXPR CTR, CO41B1, Dow Corning Corp. Midland, MI 48686-0994 From praa2@cluster1.urz.uni-halle.de Wed Feb 1 10:41:50 1995 Received: from mlucom.urz.uni-halle.de for praa2@cluster1.urz.uni-halle.de by www.ccl.net (8.6.9/930601.1506) id JAA16542; Wed, 1 Feb 1995 09:49:58 -0500 From: Received: from cluster1.urz.Uni-Halle.DE by mlucom.urz.uni-halle.de with SMTP (1.36.108.7/15.6) id AA09610; Wed, 1 Feb 1995 15:48:10 +0100 Posted-Date: Wed, 1 Feb 1995 15:49:03 +0100 (MEZ) Received-Date: Wed, 1 Feb 1995 15:48:10 +0100 Received: by cluster1.urz.uni-halle.de (AIX 3.2/UCB 5.64/4.03) id AA34629; Wed, 1 Feb 1995 15:49:04 +0100 Message-Id: <9502011449.AA34629@cluster1.urz.uni-halle.de> Subject: CCL: NBO for DFT available ? To: chemistry@ccl.net Date: Wed, 1 Feb 1995 15:49:03 +0100 (MEZ) X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 895 Dear netters, i was wondering if there is a customized interface of the NBO-tool (natural bond orbital analysis by Reed/Weinhold) for using in connection with 'native' DFT-codes (like DeFT, deMon, DGauss, ...) as available for common ab-initio/semiempirical codes (GaussianXX, GAMESS, Mopac ...). I've realized that within G92/DFT this tool is available also for dft calculations. Unfortunately I need this tool in connection with one of the above mentioned 'native' dft codes. Though the ks-orbitals do not have the same physical meaning as the canonical hf-orbitals, is such a tool reliable for the description e.g. the metal-ligand interaction ? Are there other tools (maybe density difference maps, fragment orbital analysis, ...) for a qualitative and/or quantitative analysis of such interactions ? Any suggestions or hints are grateful appreciated. Many thankx in advance Peter From nick@BCH.UMontreal.CA Wed Feb 1 11:12:57 1995 Received: from condor.CC.UMontreal.CA for nick@BCH.UMontreal.CA by www.ccl.net (8.6.9/930601.1506) id JAA16445; Wed, 1 Feb 1995 09:47:21 -0500 Received: from merck.BCH.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA27407 (5.65c/IDA-1.4.4 for CHEMISTRY@ccl.net); Wed, 1 Feb 1995 09:45:46 -0500 Received: from crysbio1.BCH.UMontreal.CA by merck.BCH.UMontreal.CA (940816.SGI.8.6.9/5.17) id OAA14910; Wed, 1 Feb 1995 14:47:26 GMT Received: by crysbio1.BCH.UMontreal.CA (931110.SGI/5.17) id AA08482; Wed, 1 Feb 95 09:47:13 -0500 Date: Wed, 1 Feb 95 09:47:13 -0500 From: nick@BCH.UMontreal.CA (Nick Blom) Message-Id: <9502010947.ZM8480@crysbio1.BCH.UMontreal.CA> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: CHEMISTRY@ccl.net Subject: CCL:Answer to my question on osmotic pressure Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Jan 31, 8:05pm, Eric Sribnick wrote: > Subject: CCL:Answer to my question on osmotic pressure > Thanks to everyone who wrote me. This answer is indicative of the kind > that I have been receiving (i.e. Nobody as of yet has told me that the > solution would not come out of the tube). > > ---------- Forwarded message ---------- > Date: Tue, 31 Jan 1995 18:51:05 -0600 (CST) > From:PEARLMAN@VAX.PHR.UTEXAS.EDU > To: heysrib@cs1.presby.edu > Subject: A question on osmotic pressure > > Hi -- > > > If the tube part was cut down lower than the point where osmotic > > pressure pushes the water up to, would water come out of the end > > of the tube? > > YES!! I've done this as a demonstration on several occasions. You > can actually get the solution to "shoot" out of the end of tube! > Of course, if you allow the solution to fall back into the beaker, > then the process grinds to a halt fairly quickly (as the concentrations > on both sides of the membrane become almost equal). But if you direct > the flow from the tube away from the beaker and lower the thistle tube > as necessary, you can almost empty the beaker. > > Have fun. > > -- Bob Pearlman > NOT ALWAYS YES!: the surface tension at the end of the tube may resist waters to spill over. -- ================================================================== Dr. Nick Blom Tel : +1-514-3436111 ext 5352 Departement de Biochimie Fax : +1-514-3432210 Universite de Montreal Email: nick@bch.umontreal.ca C.P. 6128, Station Centre-Ville Montreal, PQ, H3C 3J7 Canada ================================================================== From elewars@alchemy.chem.utoronto.ca Wed Feb 1 11:46:28 1995 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.9/930601.1506) id LAA19094; Wed, 1 Feb 1995 11:28:32 -0500 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.6.9/8.6.9) id LAA19850 for chemistry@ccl.net; Wed, 1 Feb 1995 11:28:30 -0500 Date: Wed, 1 Feb 1995 11:28:30 -0500 From: "E. Lewars" Message-Id: <199502011628.LAA19850@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: FISSION IN A FLASK There was a question on the Net today or yesterday about this. In his book "Cold Fusion: the Scientific Fiasco of the Century", Huizinga refers to an off-the record remark by one of the protagonists that palladium in an electrochemical cell may be undergoing fission. The view among physicists is probably that this kind of thing is even less likely than (electro)chemically induced fusion. Actually, *some* nuclear processes are not quite independent of chemical influences: electron capture radioactive decay, a la one of the isotopes of potassium, is clearly somewhat affected by the proximity of electrons, and thus by the chemical state of the atom. ==== E. Lewars === From jkl@ccl.net Wed Feb 1 11:54:24 1995 Received: for jkl@ccl.net by www.ccl.net (8.6.9/930601.1506) id LAA18570; Wed, 1 Feb 1995 11:09:33 -0500 Date: Wed, 1 Feb 1995 11:09:33 -0500 From: Jan Labanowski Message-Id: <199502011609.LAA18570@www.ccl.net> To: chemistry@ccl.net Subject: One more thing Cc: jkl@ccl.net One more thing... I also very much encorage students to send letter in support of CCL. One of the points which I am selling in the proposal is the educational value of the list. Sorry again for taking the bandwidth on non CC related issues... Jan Labanowski jkl@ccl.net From jkl@ccl.net Wed Feb 1 12:01:11 1995 Received: for jkl@ccl.net by www.ccl.net (8.6.9/930601.1506) id LAA18350; Wed, 1 Feb 1995 11:01:38 -0500 Date: Wed, 1 Feb 1995 11:01:38 -0500 From: Jan Labanowski Message-Id: <199502011601.LAA18350@www.ccl.net> To: chemistry@ccl.net Subject: From Coordinator - IMPORTANT Cc: jkl@ccl.net Columbus, Jan. 30, 1995 Dear Netters, I need your help, and this is serious... With the growing size and scope of the Computational Chemistry List I can no longer maintain it as a hobby. I need resources and help not only in the coordination, but also in development of the list... The current format of the list is outdated and cannot keep up with the explosive list growth, expectations of subscribers, and new exciting technologies in computer networks. Last summer I submitted a proposal for the support of the list, and though it has not yet been rejected, it has not been funded either. I am still waiting. The bottom line is this: If I do not get funding for this project, I will not be able to continue to coordinate the Computational Chemistry List. The cutoff time is scheduled for summer 1995. Obviously, I will try to find a new home for the list, but you all realize that with more than 2000 subscribers, 1 GByte/week of files ftp-ed from the CCL archives, and hundreds of WWW and gopher logins every day, the number of sites able to cope with such traffic is limited. You can help me by sending me a letter in support of the list. Not only the number but also the contents of these letters will matter. So please write why you think the list is important and why it should be supported. Please send the letters (on your organization letterhead) to me: Jan Labanowski, Ph.D. Ohio Supercomputer Center 1224 Kinnear Rd Columbus, OH 43212 It may help if you read the proposal itself. The directory /pub/chemistry/ccl-proposal has been created in the CCL archives. The following files are there 25049 summary-300dpi.ps -- 600 dpi PostScript of summary 28271 summary-600dpi.ps -- 300 dpi PostScript of summary 4855 summary.tex -- LaTeX version of summary 4874 summary.txt -- plain text version of summary 106954 proposal-300dpi.ps -- 600 dpi PostScript of proposal 111746 proposal-600dpi.ps -- 300 dpi PostScript of proposal 35464 proposal.tex -- LaTeX version of proposal 38334 proposal.txt -- plain text version of proposal You can download them via anonymous ftp (www.ccl.net), gopher (www.ccl.net, port 73), or electronic mail by sending a message: select chemistry cd ccl-proposal get summary.txt (for example) get proposal.txt quit to MAILSERV@ccl.net. These files are also accessible via the CCL home page: URL: http://www.ccl.net/chemistry.html Thank you in advance for your support, and I will appreciate your comments (but please excuse me if I am not able to answer them right away). I understand how busy you are, but this is your chance to help me save the list and transform it into a much better resource than it currently is. Jan Labanowski CCL Coordinator jkl@ccl.net -- Dr. Jan K. Labanowski, Senior Research/Supercomputer Scientist/Specialist, etc. Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212-1163 ph:(614)-292-9279, FAX:(614)-292-7168, E-mail: jkl@ccl.net JKL@OHSTPY.BITNET From rlm1003@cus.cam.ac.uk Wed Feb 1 12:41:43 1995 Received: from bootes.cus.cam.ac.uk for rlm1003@cus.cam.ac.uk by www.ccl.net (8.6.9/930601.1506) id MAA21222; Wed, 1 Feb 1995 12:35:01 -0500 Received: from apus.cus.cam.ac.uk [131.111.8.2] (ident = root) by bootes.cus.cam.ac.uk with smtp (Smail-3.1.29.0 #24) id m0rZiwx-000C08C; Wed, 1 Feb 95 17:34 GMT Received: by apus.cus.cam.ac.uk (Smail-3.1.29.0 #11) id m0rZiwx-00034NC; Wed, 1 Feb 95 17:34 GMT Message-Id: Date: Wed, 1 Feb 95 17:34 GMT From: rlm1003@cus.cam.ac.uk (Ricardo) To: CHEMISTRY@ccl.net Subject: CCL: G.L.D. Ritchie's email address Dear Netters, A friend asked me to inquire about Prof. Geoffrey L. D. Ritchie's e-mail address. He is at the Dept. of Chemistry of the University of New England in Australia. Thank you for your help. R. L. Mancera Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW, UK P.S. It would be very helpful if answers could be sent directly to the following e-mail address: jesus@papalotl.pquim.unam.mx From herbert.homeier@rchs1.chemie.uni-regensburg.de Wed Feb 1 14:41:49 1995 Received: from comsun.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by www.ccl.net (8.6.9/930601.1506) id OAA23449; Wed, 1 Feb 1995 14:39:26 -0500 Received: from rchs1.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA10452 (5.65c/IDA-1.4.4 for ); Wed, 1 Feb 1995 20:39:05 +0100 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA14619; Wed, 1 Feb 95 20:40:44 +0100 Date: Wed, 1 Feb 95 20:40:44 +0100 From: Herbert Homeier (t4720) Message-Id: <9502011940.AA14619@rchs1.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: 1995, 10: Symposium Theoretische Chemie/Elektronenstrukturmethoden Reply-To: Loccum@Nov.Theochem.Uni-Hannover.DE Dear CCLers, the following pointer to a conference (language: German) may be of interest also for you. Herbert Homeier >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 31. Symposium fuer Theoretische Chemie 10-13 Oktober 1995 in Loccum Elektronenstrukturmethoden f"ur gro{\ss}e Systeme Voranmeldung: bis 15.3.1995 Veranstalter: Prof. Dr. K. Jug Theoretische Chemie Universit"at Hannover Am Kleinen Felde 30 D-30167 Hannover Telefon: 0049/511/762-5445 Telefax: 0049/511/762-5939 Email: Loccum@Nov.Theochem.Uni-Hannover.DE Weitere Informationen dazu im WWW: http://ws2.theochem.uni-hannover.de/loccum.html <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -------------------------------------------------------------- Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX : +49-941-943 2305 email: na.hhomeier@na-net.ornl.gov HOMEPAGE --------------------------------------------------------------- From herbert.homeier@rchs1.chemie.uni-regensburg.de Wed Feb 1 14:57:58 1995 Received: from comsun.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by www.ccl.net (8.6.9/930601.1506) id NAA22826; Wed, 1 Feb 1995 13:59:46 -0500 Received: from rchs1.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA09540 (5.65c/IDA-1.4.4 for ); Wed, 1 Feb 1995 19:59:23 +0100 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA14570; Wed, 1 Feb 95 20:01:02 +0100 Date: Wed, 1 Feb 95 20:01:02 +0100 From: Herbert Homeier (t4720) Message-Id: <9502011901.AA14570@rchs1.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: Re: CCL:Fortran 90 standard Cc: kus@suearn2.bitnet Mikhail Kuzminsky -135-6388 (KUS@SUEARN2.BITNET) writes: >Dear CCLers ! > >I want find some ftp- or WWW-sites containing description of >FORTRAN 90 standard. >If this information isn't accessible, I'll be very appreciate >if somebody will send me the data containing some references to usual >articles about FORTRAN 90 . > >Thanks in advance, >Dr. Mikhail Kuzminsky, >N.D.Zelinsky Institute of Organic Chemistry, >Moscow >e-mail :kus@suearn2.bitnet A tutorial to Fortran 90 is online available: WWW: http://rchs1.chemie.uni-regensburg.de/gopher/pub/Tutorial.fortran90 gopher: gopher rchs1.chemie.uni-regensburg.de 5. Data Files # the numbers 22. Tutorial.fortran90 # might be different in # the future ftp: ftp rchs1.chemie.uni-regensburg.de Name .... : anonymous Password: < your_email_address cd pub get Tutorial.fortran90 bye For German speaking CCLers: Das Regionale Rechenzentrum fuer Niedersachsen/Universitaet Hannover gibt eine sehr lesbare Anleitung "Fortran 90 Ein Nachschlagewerk" (RRZN-Klassifikationsschluessel SPR.F90 1) heraus, das auch ueber viele Uni-Rechenzentren erhaeltlich ist. -------------------------------------------------------------- Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX : +49-941-943 2305 email: na.hhomeier@na-net.ornl.gov HOMEPAGE --------------------------------------------------------------- From wipke@SECS.UCSC.EDU Wed Feb 1 17:47:23 1995 Received: from MOLENG.UCSC.EDU for wipke@SECS.UCSC.EDU by www.ccl.net (8.6.9/930601.1506) id RAA27860; Wed, 1 Feb 1995 17:05:38 -0500 Received: by SECS.UCSC.EDU (MX V3.1C) id 7448; Wed, 01 Feb 1995 14:05:00 PST Date: Wed, 01 Feb 1995 14:04:57 PST From: "W. Todd Wipke" To: chemistry@ccl.net Message-ID: <0098B565.42BEF6DB.7448@SECS.UCSC.EDU> Subject: Summer Undergraduate Research Fellowships (SURF) Undergrad research opportunities in computational chemistry (and other areas of chemistry and biochemistry, including environmental chemistry). Details available in application materials available from "fileserv@secs.ucsc.edu" via "SEND SURF" in the BODY of your msg. Deadline 15 Feb 1995. This is for US citizens or resident aliens who are undergrad students in their junior year now. -Todd Wipke SURF Director Molecular Engineering Laboratory University of California Santa Cruz, CA 95064 From PEARLMAN@VAX.PHR.UTEXAS.EDU Wed Feb 1 18:41:41 1995 Received: from VAX.PHR.UTEXAS.EDU for PEARLMAN@VAX.PHR.UTEXAS.EDU by www.ccl.net (8.6.9/930601.1506) id SAA29530; Wed, 1 Feb 1995 18:32:56 -0500 Date: Wed, 1 Feb 1995 17:32:54 -0600 (CST) From: PEARLMAN@VAX.PHR.UTEXAS.EDU Message-Id: <950201173254.a707@VAX.PHR.UTEXAS.EDU> Subject: 1995 Gordon Research Conference on QSARs To: CHEMISTRY@ccl.net X-Vmsmail-To: SMTP%"CHEMISTRY@ccl.net" Greetings! I am writing to encourage (and facilitate) your participation in the 1995 Gordon Research Conference on Quantitative Structure-Activity Relationships which will be held in Tilton, New Hampshire (USA) between the evening of Sunday, August 6th and noon on Friday, August 11th. I have appended an abbreviated indication of the stimulating program which was organized by our Vice-Chairman, Dr. Herschel Weintraub. A more complete listing and a copy of the GRC Application Form will be published in the first February issue of _Science_. This year, for the first time, the GRC is also accepting Applications via e-mail. For your convenience, I have also appended a copy of the electronic version of the GRC Application Form. If you wish to apply via e-mail, please send a *neatly excised* copy of the appended form to: sandie@grcmail.grc.uri.edu (NOT TO ME!). Please note that both the Application Form and the abbreviated Program indicate that poster presentations by GRC attendees are encouraged. If you wish to present a poster, please be CERTAIN to append an abstract to your Application Form. Your abstract will be posted on the (4 ft by 8 ft, vertically oriented) poster-board which will be reserved in your name. This year, the standard "Fixed Fee" is $510 which includes not only the Conference registration but room (double-occupancy) and board as well. Chartered bus transportation between Boston's Logan Airport and the Conference site will be available for approximately $35 (round trip). I look forward to greeting old friends and making new friends in Tilton this summer. I hope to see you there. Sincerely, Bob Pearlman QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS (QSAR) Tilton School Tilton, NH 6 August - 11 August R. S. Pearlman, Chairman H. J. R. Weintraub, Vice-Chairman (and Program Organizer) Monday, August 7, 1994 -------------------------------------------------------------- Morning: Combinatorial Chemistry, Diversity & 3D Databases Session Chair: Y. Martin Speakers: M. Ross, J. Blaney, P. Johnson -------------------------------------------------------------- Afternoon: Combinatorial Chemistry, Diversity & 3D Databases Poster Session Chair: O. Raevsky -------------------------------------------------------------- Evening: Combinatorial Chemistry, Diversity & 3D Databases Session Chair: S. Barcza Speakers: O. Guner, D. Patterson -------------------------------------------------------------- Tuesday, August 8, 1994 -------------------------------------------------------------- Morning: Recent Applications of Traditional QSAR Session Chair: G. Famini Speakers: M. Abraham, M. Charton, P. Magee -------------------------------------------------------------- Afternoon: General Poster Session Poster Session Chair: P. Seybold -------------------------------------------------------------- Evening: Toxicity Prediction Session Chair: S. DeVito Speakers: J. Dearden, V. Gombar -------------------------------------------------------------- Wednesday, August 9, 1994 -------------------------------------------------------------- Morning: Successful Applications in Structure-Based Design Session Chair: G. Marshall Speakers: H. Moereels, K. Holloway, R. Wade -------------------------------------------------------------- Afternoon: QSAR Techniques for Structure-Based Design Poster Session Chair: C. Selassie -------------------------------------------------------------- Evening: Successful Applications in Structure-Based Design Session Chair: A. Hagler Speakers: T. Oprea, P. Goodford -------------------------------------------------------------- Thursday, August 10, 1994 -------------------------------------------------------------- Morning: Variable Selection Session Chair: S. Clementi Speakers: H. Kubinyi, J. Frazer, B. Bush -------------------------------------------------------------- Afternoon: General Poster Session Poster Session Chair: L. Hall -------------------------------------------------------------- Evening: "Nuts and Bolts" Session on the Use of Techniques Session Chair: L. Balbes Group Discussion -------------------------------------------------------------- Friday, August 11, 1994 -------------------------------------------------------------- Morning: New Technologies Session Chair: J. Wikel Speakers: G. Kellogg, D. Rogers, G. Maggiora ********* ===================== GRC Application Form ========================= >Please e-mail this application to: sandie@grcmail.grc.uri.edu > >Applications are required of all individuals participating in a Conference. >This applies to the Chair, Co-Chairs, Vice Chair, Discussion Leaders, >Speakers, Poster Presenters, and Conferees. > >DEADLINE FOR RECEIPT OF APPLICATIONS IS 6 WEEKS PRIOR TO THE CONFERENCE >----------------------------------------------------------------------- >CONFERENCE LOCATION: Tilton School, Tilton, NH >CONFERENCE NAME: Quantitative Structure-Activity Relationships (QSARs) >CONFERENCE DATE: August 6 - 11 > >NAME: >ORGANIZATION: >BUSINESS ADDRESS: >CITY: >STATE: >COUNTRY: >ZIP CODE: >PHONE: >FAX: >E-MAIL: >----------------------------------------------------------------------- >ACCOMMODATIONS FOR APPLICANT:___ > GUEST(S):___ > CHILDREN:___ >----------------------------------------------------------------------- >I work in ACADEMIC INSTITUTION:___ If predominantly undergraduate, >please check here:___ > GOVERNMENT AGENCY:___ > INDUSTRIAL CORPORATION:___ >----------------------------------------------------------------------- >Please check: CHAIR:___ > VICE CHAIR:___ > DISCUSSION LEADER:___ > SPEAKER:___ > POSTER PRESENTER:___ > ATTENDEE:___ >----------------------------------------------------------------------- >Previous conferences attended > NONE:___ > 1-5:___ > 6-10:___ > 10+:___ >----------------------------------------------------------------------- >Your Position? GRADUATE STUDENT:___ > POSTDOC:___ > RESEARCH SCIENTIST:___ > PROFESSOR:___ > RESEARCH DIRECTOR:___ > PROGRAM MANAGER:___ > OTHER:___ >----------------------------------------------------------------------- >Are you personally involved in research activities in the subject area of >the conference? (Y/N):___ > >How many papers have you published during the past three years in the >subject area of the conference?:___ >----------------------------------------------------------------------- >You are invited to submit an abstract for a poster presentation at the >Conference. Many Chairs find abstracts very useful in making decisions >concerning admissions to their Conferences. Applications are referred to >the Conference Chair in accordance with the established regulations. >Following the Chair's acceptance, the registration card will be sent to >you. Please complete and return it immediately with payment of FIXED FEE. >----------------------------------------------------------------------- >GORDON RESEARCH CONFERENCES ADMITS SCIENTIFICALLY-QUALIFIED CONFEREES OF >ALL SEX, RACE, RELIGION, AGE, COLOR, AND NATIONAL ORIGIN. >----------------------------------------------------------------------- >Indicate your particular activities which justify favorable consideration >of you as a participant in and contributor to this Conference. (Not >required of speakers and session chairs.) > > > > > > > > >----------------------------------------------------------------------- >The recording of lectures by tapes, etc. and the photography of slide >material are prohibited. Printed reference to Gordon Research Conference >papers and discussion is not permittted. Authors are requested to omit >references to the Conferences in any publication. Guests are not permitted >to attend the conference lectures and discussion sessions. > >Each member of the Conference agrees to these regulations when registration >is accepted. ************* Remember, return your application to the GRC --- NOT TO ME! Hope to see you in August. --- Bob Pearlman From elewars@alchemy.chem.utoronto.ca Wed Feb 1 21:41:37 1995 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.9/930601.1506) id VAA01699; Wed, 1 Feb 1995 21:36:54 -0500 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.6.9/8.6.9) id VAA02239 for chemistry@ccl.net; Wed, 1 Feb 1995 21:36:50 -0500 Date: Wed, 1 Feb 1995 21:36:50 -0500 From: "E. Lewars" Message-Id: <199502020236.VAA02239@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: ERROR IN INFO RE SYNTHESIS PROGRAM A few days ago, in response to a query, I said that an org synth program sold by ACS was advertised in C&EN, Sept 1994 (or 1993). The correct location is C&EN 1993 Nov 15, page 46 [an unnumbered advertisement page]. The program is SynTree, $145 for the PC or Mac version (price for ACS members). It's made by Trinity Software, PO Box 960, Campton, NH 03223; phone 603 726-4641, FAX -3781. E. Lewars ===================================== From D.Winkler@chem.csiro.au Wed Feb 1 21:45:41 1995 Received: from auric.chem.csiro.au for D.Winkler@chem.csiro.au by www.ccl.net (8.6.9/930601.1506) id VAA01554; Wed, 1 Feb 1995 21:20:57 -0500 Received: from chem.csiro.au (mac-40149.chem.csiro.au) by auric.chem.csiro.au with SMTP id AA22335 (5.67b/IDA-1.5 for chemistry@ccl.net); Thu, 2 Feb 1995 13:15:52 +1100 Date: Thu, 2 Feb 95 13:20:41 EST From: "Dr. Dave Winkler" Subject: Modelling at Chapel Hill To: chminf-l@iubvm.ucs.indiana.edu, chemistry@ccl.net X-Mailer: LeeMail 2.0.4 Message-Id: Can anyone give me names of people at Chapel Hill who do molecular modelling and drug design? I believe thay have a virtual reality setup which can be used to dock putative inhibitors into active sites. Cheers, Dave __________________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. "Life is what happens to you while you're making other plans" From olson@bioorganic.ucsb.edu Wed Feb 1 21:48:10 1995 Received: from hub.ucsb.edu for olson@bioorganic.ucsb.edu by www.ccl.net (8.6.9/930601.1506) id VAA01575; Wed, 1 Feb 1995 21:23:07 -0500 Received: from bioorganic (bioorganic.ucsb.edu) by hub.ucsb.edu; id AA12860 sendmail 4.1/UCSB-2.1-sun Wed, 1 Feb 95 18:23:02 PST for chemistry@ccl.net Received: by bioorganic (931110.SGI/930416.SGI) for @hub.ucsb.edu:chemistry@ccl.net id AA02900; Wed, 1 Feb 95 18:28:12 -0800 Date: Wed, 1 Feb 95 18:28:12 -0800 From: olson@bioorganic.mechanisms.ucsb.edu (Leif Olson) Message-Id: <9502020228.AA02900@bioorganic> To: chemistry@ccl.net Subject: Summary: MD trajectory analysis Netters: Here is a summary of the responses I got for a request for molecular dynamics trajectory analysis software. I was interested in a program which can do the same things as "Curves, Dials, and Windows", part of the "Molecular Dynamics Analysis Toolchest" of Ravishanker and Beveridge at Wesleyan University. The MD Toolchest is between versions and so is (unfortunately) temporarily unavailable. -------------------------------------------------------------------- Hi Leif, I don't know exactly what you are looking for and on which platform you plan to run the software but I have a program named SCARECROW which could be helpful. If you are interested you can have a look at it either through WWW or ftp. WWW URL: http://www.csc.fi/lul/chem/scarecrow/jmg_scare.html or Anonymous ftp from nic.funet.fi in directory /pub/sci/chem/scarecrow Regards, -leif laaksonen ------------------------------------------------------------------- Leif Laaksonen | Center for Scientific Computing | Phone: 358 0 4572378 P.O. Box 405 | Mobile: 358 400425203 FIN-02101 Espoo | Telefax: 358 0 4572302 FINLAND | Mail: Leif.Laaksonen@csc.fi ---------URL: http://laaksonen.csc.fi/leif.laaksonen.html---------- I dreamed that, as I wandered by the way, Bare winter suddenly was changed to spring. P.B. Shelley ------------------------------------------------------------------- Dear Dr. Olson You could try to run NUPARM, after separating all the coordinate files in separate pdb files, naming them as file#.pdb. The program NUPARM is available in Brookhaven Protein Data Bank, however I am sending you separately a latest version of it along with a sample c-shell script to run NUPARM for a number of coordinate files. This script would create structure data for all the coordinate files in different files, named after the coordinate file. You may use unix "grep" and "cut" commands later to pick out the selected structural parameters from the name#.prm files. Best wishes and please feel free to call me if you have any questions/problems in running this program. Dhananjay Bhattacharyya bhatta@par12.mgsl.dcrt.nih.gov ----------------------------------------------------------------------- I have an analysis program which you can script to run at the end of whatever cycles, it doesn't output like dials and window but it does give all complementary parameters and Cartesian and helical parameters from the local view between neighboring bases and basepairs. I had articles in last years JMB and JBSD. Let me know if a single run program with comparable parameters is what you can use. Marla Babcock MARLA@chemf.rutgers.edu ----------------------------------------------------------------------- My impression is that Curves/dials/windows is for analyzing trajectories generated w/ dynamics programs, rather than being a dynamics program per se. See our Web page for a reference to SCARECROW, another analysis package. See: http://www.amber.ucsf.edu/amber/amber.html Bill Ross ross@cgl.ucsf.edu ------------------------------------------------------------------------ Dr Olson: I read your posting on CCL. Our lab along with Dr. David Doherty has developed a program called MOLSIM. It may help resolve your problem. Following is an excerpt from its manual, "The mda module The mda option of Molsim is an interactive MD analysis facility, which operates on either the trajectory files output by mdsim or the energy files output by mdsim (choose "none" upon starting up mda). Some of the types of analysis provided by mda include: saving of a particular frame of the trajectory file to a molecule file; bond length, bond angle, torsion angle, or atom-atom distance monitoring and averaging over the course of the trajectory; calculation of thermodynamic properties (assuming a canonical ensemble and an equilibrium trajectory) from the energy files output by mdsim (choose "none" when mda asks for a trajectory file definition); calculation of certain polymer properties from the trajectory; and more. mda can act upon several consecutive trajectories, treating them as one continous trajectory. This is accomplished by creating a text file which contains the name of each of the trajectory files on a separate line, then choosing "multiple" when mda starts up." MOLSIM software is a commercial program. If you wish furthur information, please let me know. You can also directly contact Dr. Doherty(doherty@msc.edu) or Dr. Hopfinger(u32583@uicvm.uic.edu). Good Luck, Hitesh C.Patel Laboratory of Molecular Modeling and Design College of Pharmacy Univ. of Illinois at Chicago 833 S. Wood St., m/c 781, #539 Chicago, IL 60612 312 996 6002 312 996 6004 fax: 312 996 7107 ------------------------------------------------------------------------- -We are looking at some of these packages now. We have about 13,000 DNA molecular dynamics structures in CHARMm DCD files, so we need to reduce the data to digestible chunks for understanding and publication. So far, the easiest way to this still appears to be Curves, Dials and Windows, but some of the other programs have some very intriguing features that we can probably use for future analyses of biomolecular structures. Thanks very much to the respondents! ------------------------------------------------------------------------- Leif P. Olson, Ph.D. | phone: 805-893-2234 (Bruice Lab) | UC Santa Barbara Chemistry Dept.| olson@bioorganic.ucsb.edu "Yes, it does rain in Southern California" ------------------------------------------------------------------------- From SUTJIANTO@cmt.anl.gov Wed Feb 1 22:41:38 1995 Received: from anlcmt.cmt.anl.gov for SUTJIANTO@cmt.anl.gov by www.ccl.net (8.6.9/930601.1506) id WAA02210; Wed, 1 Feb 1995 22:32:04 -0500 Date: Wed, 1 Feb 1995 21:31:54 -0600 (CST) From: Amin Sutjianto To: CHEMISTRY@ccl.net Message-Id: <950201213154.2020e661@cmt.anl.gov> Subject: point charge Hi Netters, Could you tell me whether there is any other program, beside GAUSSIAN9*, which includes point charges around a quantum mechanic cluster? I appreciate very much for your help. Amin From osawa@cochem.tutkie.tut.ac.jp Wed Feb 1 23:41:42 1995 Received: from cochem.cochem.tutkie.tut.ac.jp for osawa@cochem.tutkie.tut.ac.jp by www.ccl.net (8.6.9/930601.1506) id WAA02569; Wed, 1 Feb 1995 22:59:35 -0500 Received: from [133.15.160.31] by cochem.cochem.tutkie.tut.ac.jp (8.6.9+2.4Wb/6.4JAIN) id MAA10667; Thu, 2 Feb 1995 12:33:59 +0900 Date: Thu, 2 Feb 1995 12:33:59 +0900 Message-Id: <199502020333.MAA10667@cochem.cochem.tutkie.tut.ac.jp> To: chemistry@ccl.net From: osawa@cochem.tutkie.tut.ac.jp (Eiji Osawa) Subject: Peter Kollman's address? MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.5-J10) Does anyone know Professor Peter Kollman's e-mail address. With many thanks, Eiji Osawa /************************************************* * Eiji Osawa * Department of Knowledge-based Information Engineering * Toyohashi University of Technology * Aichi 441, Japan * Phone: x-81-532-47-0111(ex. 853) * FAX: x-81-532-48-5588 * E-mail: osawa@cochem.tutkie.tut.ac.jp *************************************************/