From chemistry-request@www.ccl.net Wed Sep 16 08:42:14 1998 Received: from sunny.mpimf-heidelberg.mpg.de (sunny.mpimf-heidelberg.mpg.de [149.217.50.30]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA27709 Wed, 16 Sep 1998 08:41:50 -0400 (EDT) Received: from [149.217.50.47] (mac20 [149.217.50.47]) by sunny.mpimf-heidelberg.mpg.de (8.8.8/8.8.8) with ESMTP id OAA29486; Wed, 16 Sep 1998 14:30:46 +0200 (MET DST) Message-Id: In-Reply-To: <9809131414.ZM3019@hamilton.math.missouri.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 16 Sep 1998 14:42:57 +0200 To: "Don Steiger" , chemistry@www.ccl.net From: Eberhard von Kitzing Subject: Re: CCL:Multi-time scale integration. Dear Don Steiger, At 14:14 Uhr -0500 13.09.1998, Don Steiger wrote: >In the literature on multi-time scale integration, a lot of importance is >placed >on time reversibility. Why this is so important is something that I have >never >been able to figure out. If an integration algorithm is efficient and >produces >a small global error then why is this not sufficient. If anybody can >enlighten >me on this subject I would appreciate it. Because Newton's equations of motions are invariant under time reversal any integrator should reproduce this behavior which is closely related to energy conservation. ====================================================================== Eberhard von Kitzing Max-Planck-Institut fuer Medizinische Forschung Jahnstr. 29 D 69115 Heidelberg Germanny email: vkitzing@silia.mpimf-heidelberg.mpg.de WWW: http://sunny.mpimf-heidelberg.mpg.de/people/vkitzing/ From chemistry-request@www.ccl.net Wed Sep 16 14:01:39 1998 Received: from argus.chemnet.ee (argus.chemnet.ee [193.40.250.66]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA01522 Wed, 16 Sep 1998 14:01:37 -0400 (EDT) Received: from boc.ic.ee (boc.ic.ee [193.40.63.200]) by argus.chemnet.ee (8.7.4/8.7.3) with SMTP id UAA12789; Wed, 16 Sep 1998 20:00:27 +0300 Received: from argus.chemnet.ee by boc.ic.ee id aa04125; Wed, 16 Sep 98 19:54:08 estonia Received: by localhost with Microsoft MAPI; Wed, 16 Sep 1998 21:05:14 +0300 Message-ID: <01BDE1B5.B2D3B130.ivarm@boc.ic.ee> From: Ivar Martin Reply-To: "ivarm@boc.ic.ee" To: "'Juan Frau'" , "chemistry@www.ccl.net" Subject: RE: NMR software Date: Wed, 16 Sep 1998 21:05:12 +0300 Organization: Keemia Instituut X-Mailer: Microsoft Internet E-mail/MAPI - 8.0.0.4211 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear Juan, Distance geometry program DGEOM95 can do the job you mentioned below. It is available from QCPE. Authors: Jeffrey M. Blaney, Gordon M. Crippen, Andrew Dearing, J. Scott Dixon, David C. Spellmeyer 1984-1995. > We are planning to get the conformation of some structures using > parameters obtained from NOE calculations. > > We would like to know which kind of software could be useful for > this job. > Thanks in advance. All the best! Ivar Martin, Ph.D Department of Bioorganic Chemistry Institute of Chemistry Tallinn Technical University Akadeemia tee 15, EE0026 Tallinn, ESTONIA Phone: +(372 2) 526510 Fax: +(372 2) 526513 E-mail: ivarm@boc.ic.ee From chemistry-request@www.ccl.net Wed Sep 16 14:07:41 1998 Received: from postal.ucc.uno.edu (postal.ucc.uno.edu [137.30.1.80]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA01564 Wed, 16 Sep 1998 14:06:52 -0400 (EDT) Received: from slater (slater.chem.uno.edu) by postal.ucc.uno.edu (PMDF V5.1-10 #D3297) with SMTP id <0EZE00LDR21DW0@postal.ucc.uno.edu> for chemistry@www.ccl.net; Wed, 16 Sep 1998 13:00:49 -0500 (CDT) Date: Wed, 16 Sep 1998 12:59:43 -0500 From: Howard Alper Subject: Re: Parameterization Sender: heacm@slater.chem.uno.edu To: chemistry@www.ccl.net Cc: halper@uno.edu Message-id: <35FFFC8F.6F59@uno.edu> Organization: University of New Orleans MIME-version: 1.0 X-Mailer: Mozilla 3.0 (X11; U; AIX 1) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit Hello, I'm sorry if this is a repeat, but as far as I could tell this message did not post when I originally sent it - twice. Several weeks back I wrote about parameterization and units in simulation (still waiting for some replies...) Now I have some questions about parameterization to create forcefields for MD simulations. Specifically, I am interested in parameterizing Nitromethane. While any information regarding a set of parameters (bond, angle, torsion, out-of-plane,charges,van der Waals, etc) would be welcome, we are interested in generating the neccesary parameters, and in a form suitable for use in CHARMM. To this end I have several questions: 1) I need to derive, somehow, structural parameters and force constants for bond-stretching and angle-binding. The force constants should be in units of energy/(angstroms**2) and energy/(radian**2) (I have seen some force constants in old papers that give force constants in units of millidynes/angstroms, but I do not understand how that relates to the case of angle-bending constants...) I can perform an optimization and frequency calculation in Gaussian, for example, but from what I can tell the resulting frequencies and force constants are for the normal modes of the molecule, not bonds and angles/etc. Does anyone know if Gaussian has any options to derive the type of force constants I require? Or, does anyone know of a post-Gaussian analysis program that would do the above? 2) I also need to derive van der Waals parameters. One person I asked said something on the order of "you can derive that from the interaction of two nitromethane molecules". To a parameterization novice, that is not very specific advice. Could anyone clarify what in detail needs to be done, provide references, describe how programs like Guassian might be used to get VDW parameters, etc? (If one calculates the interaction energy of two nitromethane molecules at verious distances and orientations, is not the total energy for a configuration the sum of coulombic and VDW terms? Does that mean the charges must first be derived?) Thanks in advance, Howard Alper -- Howard E. Alper, Ph.D. Dept. of Chemistry and The Advanced Materials Research Institute University of New Orleans New Orleans, LA 70148 504-280-7216 - Helping molecules find happiness for almost a 5th of a century. From chemistry-request@www.ccl.net Wed Sep 16 15:23:16 1998 Received: from org.chem.msu.su (org.chem.msu.su [158.250.32.94]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA03468 Wed, 16 Sep 1998 15:23:15 -0400 (EDT) Received: from org.chem.msu.su (org-qsar7.chem.msu.su [158.250.48.104]) by org.chem.msu.su (8.8.8/8.8.8) with ESMTP id XAA14708; Wed, 16 Sep 1998 23:22:11 +0400 (MSD) (envelope-from serge@org.chem.msu.su) Message-ID: <36001027.C0AF1D23@org.chem.msu.su> Date: Wed, 16 Sep 1998 23:23:20 +0400 From: Serge Pisarev Reply-To: screwdriver@innocent.com Organization: Moscow State University X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: Ricardo Longo CC: CHEMISTRY@www.ccl.net Subject: Re: CCL:x-ray to cartesian References: <35FE62AC.37EC64DF@npd.ufpe.br> Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit > Dear Netters, > > Does anybody has a program that converts x-ray coordinates > (symmetry + fractional coordinates of the unique atoms) into > cartesian coordinates for the unit cell? I know that Ortep3 > can plot the x-ray coordinates, but I cannot make to write up > the cartesians of the unit cell. > Thanks a lot. Ricardo Longo Try RICON from ftp://org.chem.msu.su/pub/software/ricon/ Hope it helps with best regards -- Serge ^^^^^^^^__,,,_(@)_(@)_,,,___^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Serge Pisarev -- Computational Chemistry, Dept. of Organic Chemistry, Moscow State University, Moscow, Russia email : serge@org.chem.msu.su WWW : http://org.chem.msu.su/~serge From chemistry-request@www.ccl.net Wed Sep 16 18:39:57 1998 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA06566 Wed, 16 Sep 1998 18:39:57 -0400 (EDT) Received: from redox.scripps.edu (redox.scripps.edu [137.131.240.50]) by relay1.scripps.edu (8.9.1a/TSRI-2.5r) with ESMTP id PAA07844 for ; Wed, 16 Sep 1998 15:39:57 -0700 (PDT) Received: from localhost (jesusmc@localhost) by redox.scripps.edu (8.8.5/TSRI-1.4) with SMTP id PAA08891 for ; Wed, 16 Sep 1998 15:39:55 -0700 (PDT) Date: Wed, 16 Sep 1998 15:39:55 -0700 (PDT) From: "Jesus M. Castagnetto" Sender: jesusmc@scripps.edu To: Computational Chemistry List Subject: Re: MEAD Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, Below is the response that Dr. Bashford sent to Fernando L. Barroso w/ respect to his questions about MEAD. Dr. Bashford asked me to also forward this to the CCL list. Regards. ===== Jesus M. Castagnetto, Ph.D. - jesusmc@scripps.edu TSRI, Dept. of Molecular Biology |"Activation Energy: The useful 10550 N. Torrey Pines Rd. MBP326 | quantity of energy available La Jolla, CA 92037 | in one cup of coffee." Phone: 619-784-8582 Fax: 619-784-2289 Lab: http://www.scripps.edu/research/metallo/ MetalloDB: http://metallo.scripps.edu/index.html Pilot Stuff: http://www.geocities.com/ResearchTriangle/Lab/1059/ ---------- Forwarded message ---------- Date: Wed, 16 Sep 1998 14:58:59 -0700 From: Don Bashford To: Fernando Luis Barroso da Silva Cc: jesusmc@gage.scripps.edu, bashford@gage.scripps.edu Subject: Re: MEAD Dear Fernando, Here are the answers to your questions. A freind tells me you posted to the Comp Chem list also, so I'll have him post my answer there too. Don --------- The references for MEAD are: D. Bashford & K. Gerwert (1992) "Electrostatic Calculations of the pKa Values of Ionizable Groups in Bacteriorhodopsin" J. Mol. Biol. vol. 224 pp. 473-486 D. Bashford. "An Object-Oriented Programming Suite for Electrostatic Effects in Biological Molecules" In Yutaka Ishikawa, Rodney R. Oldehoeft, John V. W. Reynders, and Marydell Tholburn, editors, "Scientific Computing in Object-Oriented Parallel Environments", volume 1343 of Lecture Notes in Computer Science, pages 233--240, Berlin, 1997. ISCOPE97, Springer. The first one is mainly a description of pK calculations, but it is the first paper where we announce the existence and availability of MEAD. The second one is an outline of the design of the MEAD programs, and how "object-oriented" ideas were used. If the second one is not in your library, I can email you the LaTeX source for it. The MEAD distribution itself has a README file that tells how to use the programs. Otherwise, that's it for documentation. I'd like to write some, including a detailed description of internals, but it's hard to find the time. There is not yet a MEAD mailing list, but I have been keeping the email addresses names of people who contact me about MEAD so that a list could be started. Do people think there *should* be a MEAD mailing list? The distributed version of MEAD does not include support for the non-linear Poisson Boltzmann equation, but I do have an "in house" experimental implementation of NLPB, which just requires compiling and linking a few more files to the existing base of code. If anyone is really interested in playing with this (which would probably require some tinkering with the code), I'll it to them. Donald Bashford bashford@scripps.edu From chemistry-request@www.ccl.net Wed Sep 16 23:01:48 1998 Received: from jason03.u.washington.edu (root@jason03.u.washington.edu [140.142.77.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id XAA07925 Wed, 16 Sep 1998 23:01:47 -0400 (EDT) Received: from saul9.u.washington.edu (mathomps@saul9.u.washington.edu [140.142.82.7]) by jason03.u.washington.edu (8.8.4+UW97.07/8.8.4+UW98.06) with ESMTP id UAA28310 for ; Wed, 16 Sep 1998 20:01:48 -0700 Received: (from mathomps@localhost) by saul9.u.washington.edu (8.8.4+UW97.07/8.8.4+UW98.06) id UAA23200 for chemistry@www.ccl.net; Wed, 16 Sep 1998 20:01:48 -0700 (PDT) Date: Wed, 16 Sep 1998 20:01:48 -0700 (PDT) From: Mark Thompson Message-Id: <199809170301.UAA23200@saul9.u.washington.edu> To: chemistry@www.ccl.net Subject: Download ArgusLab 1.0 beta ArgusLab 1.0 Beta distribution ****************************** Molecular modeling software for Windows NT. The initial beta distribution of ArgusLab 1.0 is currently open for anyone to download and try. You can download it from: http://weber.u.washington.edu/~mathomps/ArgusLab/index.htm ArgusLab is a graphical user interface to the Argus computational chemistry program. The initial beta version is a time limited release that will function until the end of the year, by which time I plan to have the final 1.0 version in distribution. I would greatly appreciate constructive criticism. Use the questions I've included in the readme.txt file for formulating your responses and tests. Please make sure to read the license information when you install. This software is protected by copyright. Current Feature Set: --------------------- Quantum mechanical methods: AM1, PM3, MNDO, EHT, INDO/s Single-point energies, optimize geometries, electronic absorption spectra. Dipole moments, Mulliken and ZDO charges, Wiberg bond orders. Multi-threaded: can run several calculations simultaneously. Takes advantage of multiprocessor PCs. Graphics: multiple rendering styles, virtual trackball for manipulating the molecule. Display of geometry monitors and atomic labels. Size limit: None (other than the available addressible memory on your machine). File formats: currently supports only .xyz formats for reading and saving molecule structures. System Requirements: -------------------- Windows NT 4.0 Mouse ~2-5 mbytes of disk space. 16 mbytes of memory (32 or more highly recommended) (Recommended) Graphics card that supports OpenGL acceleration. Please send all suggestions, comments, bug reports to Mark Thompson at mathomps@u.washington.edu Enjoy, Mark From chemistry-request@www.ccl.net Thu Sep 17 06:58:06 1998 Received: from bobino.sefmedia.com (bobino.sefmedia.com [207.164.6.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id GAA09223 Thu, 17 Sep 1998 06:58:05 -0400 (EDT) Received: from ppp-annex-0702.mtl.total.net (ppp-annex-0702.mtl.total.net [205.205.162.156]) by bobino.chemcomp.com (NTMail 3.03.0014/1.af4w) with ESMTP id ca013782 for ; Thu, 17 Sep 1998 06:57:43 -0400 Received: by zman with Microsoft Mail id <01BDE209.2D87CEE0@zman>; Thu, 17 Sep 1998 07:02:48 -0400 Message-ID: <01BDE209.2D87CEE0@zman> From: Bill Hayden To: "'chemistry@www.ccl.net'" Subject: JCCG Date: Thu, 17 Sep 1998 07:02:22 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit CCLers: The latest edition of the Journal of the Chemical Computing Group is available at: http://www.chemcomp.com. This new issue contains features and articles on: Binary QSAR: A New Technology for HTS and UHTS Data Analysis X-Ray, Neutron and Electron Diffraction Simulations in MOE Electrostatic Fields and Surfaces in MOE QuaSAR-Cluster: A Different View of Molecular Clustering Thanks, Bill William A. Hayden Vice President Chemical Computing Group Inc. hayden@chemcomp.com 514 393 1055 From chemistry-request@www.ccl.net Thu Sep 17 07:15:24 1998 Received: from conrad.appstate.edu (dsb.appstate.edu [152.10.1.50]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA09317 Thu, 17 Sep 1998 07:15:24 -0400 (EDT) Received: from spd5.appstate.edu (SYSTEM@spd5.appstate.edu [152.10.1.31]) by conrad.appstate.edu (8.8.8/8.8.8) with ESMTP id HAA13688 for ; Thu, 17 Sep 1998 07:15:23 -0400 (EDT) Received: from dft ("port 2115"@dft.chem.appstate.edu) by conrad.appstate.edu (PMDF V5.1-12 #26327) with SMTP id <01J1WKU508I2B8KLB2@conrad.appstate.edu> for CHEMISTRY@www.ccl.net; Thu, 17 Sep 1998 07:15:21 EST Date: Thu, 17 Sep 1998 07:15:34 -0400 From: Steve Williams Subject: Re: CCL:Hartree Fock enegy X-Sender: willsd@pop.appstate.edu To: CHEMISTRY@www.ccl.net Message-id: <3.0.32.19980917071534.00b62380@pop.appstate.edu> MIME-version: 1.0 X-Mailer: Windows Eudora Pro Version 3.0 (32) Content-type: text/plain; charset="us-ascii" At 03:03 PM 9/14/98 +0000, you wrote: > >Hi ccl'ers >Could someone tell me /point me in the right direction as to where I >can find a reference as to conversion of Hartree Fock energy to >KJ/mol. A reference would also be much appreciated. >Many thanks > > 1 hartree is 627.5095 kcal/mol, and 1 kcal is 4.184 kJ exactly. > >--- >Administrivia: This message is automatically appended by the mail exploder: >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 >--- > > ***************************************** Steve Williams F F F Chemistry \ / \ / Appalachian State University Al Al Boone, NC 28608 / \ / \ USA F F F willsd@appstate.edu 828-262-2965 From chemistry-request@www.ccl.net Thu Sep 17 09:33:34 1998 Received: from mx03.uni-tuebingen.de (root@mx03.uni-tuebingen.de [134.2.3.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA09828 Thu, 17 Sep 1998 09:33:31 -0400 (EDT) Received: from theseus (theseus.pharm.chemie.uni-tuebingen.de [134.2.68.91]) by mx03.uni-tuebingen.de (8.8.8/8.8.8) with SMTP id PAA16673 for ; Thu, 17 Sep 1998 15:33:21 +0200 Date: Thu, 17 Sep 1998 15:33:21 +0200 Message-Id: <199809171333.PAA16673@mx03.uni-tuebingen.de> X-Sender: cpcmu01@cpcmu01.mail.uni-tuebingen.de X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Inge Muszynski Subject: Prospectives in Drug Design Dear CCL'lers, has anybody heard about the series "Prospectives in Drug Discovery and Design" published in Kluver/Escom? Where are those paperbacks available? How many volumes do exist and what are their titles? Many thanks in advance. Inge Muszynki Pharmaceutical Institute Auf der Morgenstelle 8 University of Tuebingen 72076 Tuebingen From chemistry-request@www.ccl.net Thu Sep 17 09:42:55 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA09874 Thu, 17 Sep 1998 09:42:55 -0400 (EDT) Received: from europe.std.com (europe.std.com [199.172.62.20]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id JAA09481 for ; Thu, 17 Sep 1998 09:42:54 -0400 (EDT) Received: from world.std.com by europe.std.com (8.7.6/BZS-8-1.0) id JAA24788; Thu, 17 Sep 1998 09:42:55 -0400 (EDT) Received: by world.std.com (TheWorld/Spike-2.0) id AA05312; Thu, 17 Sep 1998 09:42:55 -0400 Date: Thu, 17 Sep 1998 09:42:55 -0400 From: jle@world.std.com (Joe M Leonard) Message-Id: <199809171342.AA05312@world.std.com> To: chemistry@ccl.net Subject: Reading Mac 3.5's on PC's... Folks, Like many, I suspect, I'm facing replacing an OLD Mac, and since I have this large pile of floppies and datafiles... Is there any utility program which can read Mac floppies on a PC? If so, where can I get a copy...? Thanks in advance! Joe Leonard jle@world.std.com From chemistry-request@www.ccl.net Thu Sep 17 10:49:00 1998 Received: from serv1.grenet.fr (serv1.grenet.fr [193.54.185.99]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA10813 Thu, 17 Sep 1998 10:48:57 -0400 (EDT) Received: from mailhost.cermav.cnrs.fr (cermav20.cermav.cnrs.fr [195.83.29.129]) by serv1.grenet.fr (8.8.8/jtpda-5.2.9.2) with ESMTP id QAA12311 for ; Thu, 17 Sep 1998 16:46:50 +0100 (WET DST) Received: from sauterne (sauterne [195.83.29.69]) by mailhost.cermav.cnrs.fr (8.8.8/jtpda-5.3) with SMTP id QAA19640 for ; Thu, 17 Sep 1998 16:55:06 +0200 (MET DST) Sender: swaren@cermav.cnrs.fr Message-ID: <36011A5E.41C6@cermav.cnrs.fr> Date: Thu, 17 Sep 1998 16:19:10 +0200 From: Peter Swaren X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Re: CCL:Some questions about MEAD References: Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Fernando Luis Barroso da Silva wrote: > > Dear ALL, > > I would like some information about MEAD program: > > (a) Is there any "good" reference for MEAD software > (Macroscopic Electrostatics with Atomic Detail, > written by D. Bashford) ? > --I think the original reference is: Bashford D & Karplus M (1990) pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry 29:10219-10225. --You could also check: Bashford D & Gerwert K (1992) Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin. J Mol Biol 224:473-486. > (b) Is there an e-mailing list about MEAD ? --I don't know. > > (c) I also would be very grateful if somebody can tell > me if MEAD works with the linearized Poisson-Boltzmann > equation or the non-linearized form. > --To my knowledge MEAD solves the linearized PBE. Regards, - Peter - ================================================================= CENTRE DE RECHERCHES SUR LES MACROMOLECULES VEGETALES Peter Swarén Structure, Interaction et Dynamique des Oligo- et Polysaccharides C.E.R.M.A.V. - C.N.R.S. Tel: +33 4 76 03 76 49/ BP 53 76 53 F-38041 Grenoble CEDEX 9 Fax: +33 4 76 54 72 03 France E-mail: swaren@cermav.cnrs.fr ================================================================= From chemistry-request@www.ccl.net Thu Sep 17 11:48:58 1998 Received: from chem.chem.rochester.edu (root@chem.chem.rochester.edu [128.151.176.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA15127 Thu, 17 Sep 1998 11:48:58 -0400 (EDT) Received: from markov.chem.rochester.edu (markov.chem.rochester.edu [128.151.176.16]) by chem.chem.rochester.edu (8.8.5/8.8.5) with SMTP id LAA00131 for <@chem.chem.rochester.edu:CHEMISTRY@www.ccl.net>; Thu, 17 Sep 1998 11:44:16 -0400 (EDT) Received: by markov.chem.rochester.edu (920330.SGI/920502.SGI.AUTO) for @chem.chem.rochester.edu:CHEMISTRY@www.ccl.net id AA13672; Thu, 17 Sep 98 11:48:58 -0400 Date: Thu, 17 Sep 1998 11:48:54 -0400 (EDT) From: Sergei Tretiak To: computational chemistry list Cc: computational chemistry list In-Reply-To: <35BF904F.3F54@smb.chem.niu.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleague: 1. I have a question about molecular builders. We already have Gaussian and Gamess on our Unix machines. In addition we are planning to buy some program for building structures and visualization of molecules (up to hundreds heavy atoms) and calculated properties like vibrations, densities, etc. For example, possible candidates are Spartan, Gaussian View. Does anyone have experience with such program, the information would be greatly appreciated and summarized. Which program is better? Unix or windows? (I mean, for example, whether Spartan 5.0 is much better Spartan PC Plus?) 2. I did not get any messages from CCL for last couple weeks. I wander what is going on. Whether CCL activity is slowed down or my name has been slipped out of the list. I miss CCL very much. Sincerely, Sergei .-----------------------------------------------------------------------. |\ / \ | Sergei Tretiak | / \ /| |.\/...\|.......................................................|/...\/.| | Department of Chemistry | Voice: (716) 275-8289 | | University of Rochester | Fax: (716) 473-6889 | | P. O. Box 270216 | E-mail: serg@markov.chem.rochester.edu | | Rochester, NY 14627-0216 | serg@wigner.chem.rochester.edu | | Homepage: http://markov.chem.rochester.edu/serg/welcome.html | |_______________________________________________________________________| From chemistry-request@www.ccl.net Thu Sep 17 14:44:20 1998 Received: from srv01s4.cas.org (srv01s4.cas.org [134.243.50.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id OAA21132 Thu, 17 Sep 1998 14:44:19 -0400 (EDT) Date: Thu, 17 Sep 1998 14:43:43 -0400 From: wfisanick@cas.org (wxf07) Message-Id: <9809171443.AA15655@cas.org> Subject: 99.03.21 ACS Symposium - Data Mining Chemical Information Databases To: chemistry@www.ccl.net Cc: wfisanick@cas.org The ACS Division of Chemical Information is organizing a symposium on "Data Mining Chemical Information Databases" for the Spring 1999 American Chemical Society meeting to be held in Anaheim CA, March 21-25 1998. The symposium is co-sponsored by the ACS Divison of Computers in Chemistry. This symposium will focus on techniques for data mining databases of textual or textual and substance representation chemical information. Data mining can be viewed as the process of analyzing databases to automatically discover and extract relationships and, typically, to make predictions based on these relationships. Data mining techniques are being increasingly used for trend analysis and in support of scientific and business decisions. An example of a chemistry-related use is substance-property relationship discovery. Some of the techniques used in chemical information data mining include similarity search and clustering, expert systems, neural nets, genetic algorithms, and classification trees. Also, methods are needed to verify the accuracy and reliability of the discovered relationships and the subsequent predictions. Papers are invited which discuss the use of such mining and verification techniques involving aspects of textual chemical information. If you are interested in submitting a paper for this symposium, please e-mail the title of your paper by October 9th, if possible. The due date for the ACS abstract is November 16th. Also, if possible, please use the electronic version of the ACS abstract which can be obtained from http://www.acs.org/meetings/abstract/absdown.html Bill Fisanick *--------------------------*------------------------*------------------------* |William Fisanick |2540 Olentangy River Rd.|email:wfisanick.@cas.org| |Senior Scientist, Research|Columbus, OH 43202-1505 |phone:614-447-3600 x2327| |Chemical Abstracts Service|USA |fax :614-447-3813 | *--------------------------*------------------------*------------------------* From chemistry-request@www.ccl.net Thu Sep 17 16:39:45 1998 Received: from dfw-ix12.ix.netcom.com (dfw-ix12.ix.netcom.com [206.214.98.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA23262 Thu, 17 Sep 1998 16:39:45 -0400 (EDT) Received: (from smap@localhost) by dfw-ix12.ix.netcom.com (8.8.4/8.8.4) id PAA27591 for ; Thu, 17 Sep 1998 15:39:15 -0500 (CDT) Received: from bst-ma4-12.ix.netcom.com(205.186.73.140) by dfw-ix12.ix.netcom.com via smap (V1.3) id rma027453; Thu Sep 17 15:38:48 1998 Received: by localhost with Microsoft MAPI; Thu, 17 Sep 1998 16:40:34 -0400 Message-ID: <01BDE259.E4785520.kmtakita@knowledgefoundation.com> From: Kim Takita To: "'Computational Chemistry List (CCL)'" Subject: Combinatorial/New Materials Survey responses Date: Thu, 17 Sep 1998 16:34:06 -0400 X-Mailer: Microsoft Internet E-mail/MAPI - 8.0.0.4211 Encoding: 65 TEXT, 73 UUENCODE X-MS-Attachment: WINMAIL.DAT 0 00-00-1980 00:00 Thank you very much to those who submitted questions for our Industry Survey on Combinatorial & other New Materials Discovery Technologies. Thanks also to those who asked to participate in the survey! These will be sent out within the next 2 weeks. Meanwhile, here are the specific questions which were submitted by the groups. There is still time to request a survey :) Results will be compiled prior to the Combinatorial Approaches conference in Jan. -- participants will get a free copy of the results. Here are the questions: What is cost/time for each experimental point relative to conven- tional experimentation? How do the microanalytical measurements for polymers compare to those ran on the same catalyst on a macroscale sample prepared in laboratory large scale reactor. Same question but as compared to continuous reactors such as pilot plants and commercial reactors. How do you develop discrimination tools for the variables under study to help guide the research effort? Is this an Edisonian approach made more efficient? How difficult or facile is the patenting process for combinatorial chemistry? Does this imply, for example, easier composition of matter type patents? Can this technique by linked to molecular modeling to guide the development process? How expensive is it to develop Combichem in house versus on a contract basis? ----------- I want to know what kind role the photonic polymer materials will be taken in the coming century ----------- Why can't industry do this alone: why should the Federal Government use taxpayer money to fund private industry's entry into combinatorial methodologies? ----------- One of the key questions, I believe, refer to methodology and organization: How flexible (in terms of internal movements of personnel from one project to another, and in terms of leaving a project at a standstill to take another one) should an R&D organization be? How multidisciplinary should working groups be? (multidiscipline means richness of ideas and methodologies, but also means hardship in inter-work and organization; where is the optimum point?). If you read DuPont's experience and Dow's, it seems a lot had to do with these issues. ----------------------- Are you: a. now doing, or b. would you like to do polymer plus additive(s) formulation using combinatorial type techniques (non-pharmaceutical, non-agricultural, non-biological materials/polymers/additives/formulations)? ----------------------- methods for Use in inorganics ------------------------------------------------------------------------ ---------- Kim Takita Vice President The Knowledge Foundation, Inc. 101 Merrimac Street Boston, MA 02114 Phone: 617-367-7979 ext. 202 Fax: 617-367-7912 E-Mail: kmtakita@knowledgefoundation.com http://www.knowledgefoundation.com begin 600 WINMAIL.DAT M>)\^(B,4`0:0" `$```````!``$``0>0!@`(````Y 0```````#H``$(@ <` M& ```$E032Y-:6-R;W-O9G0@36%I;"Y.;W1E`#$(`0V ! `"`````@`"``$$ MD 8`> $```$````,`````P``, (````+``\.``````(!_P\!````A@`````` M``"U.\+ +'<0&J&\" `K*E;"%0```'C&D]"6&=(1I%\`X)@!V;'D@P`````` M`($K'Z2^HQ 9G6X`W0$/5 (`````0V]M<'5T871I;VYA;"!#:&5M:7-TN*]`1X`< `!````+0```$-O;6)I;F%T;W)I86PO3F5W($UA=&5R:6%L M<7,P=M`H,V%JP417U_"H (SPG9`H *@0YQ"V!N^0X0,#,4X L* M$[(!T!D0(1* ;FL@>0A@('8A!)!Y(&UU$G @=))O(2!H;Q*P('TBX&,%(":A( N (5$AH/,B M`"1R(2 ?X0>0(:$#$/T#(&(KX0GP!4 (8 5 `_!C(6 KE6YE> 5 $N!W[PG@ M*/ HD 7090!P(< #$/AE+" F$2&@"L AH"O#_G %D :0#> BF2_A(0$O('LP M<2((8B# *\()P A@ Y`?IP)*%F M*[,@+_\V4R-" M+[ A`2[ ,3 %$ > \P(P):%P;PN !4 $J Y`S"C;TF'W2%5<@.1),$KPV$V<4U@_T>Q%Y$DLC=0`,$#8 3P M!T"O47,+4"&@%S!E3W)D3^A_*Y$+8 ;@4. E82# "V!R_SZ (?!3(QR@`- E M82]Q!A#_-G$BIBTP+=$J0$\V5%E(Y/DBX&YU"& $(%:E-=$@\O]883E!)? J MP!XQ.&$`<"* _SD13O$K("6A6I8T=DOU(%+W#G @D!PP<$P@)T%'824RWU?B M(3 &\",D*\)V"L ','L"8 >1=2/0!)!/Z!>@=2YD,[$A0"80;%]P9W7^:0YP M/Z8OL%T`1P$.D!Q!GC\CL 0@+B%<4B!%7Y'K`B ',&Y/Z&$[95*Q9 '_!& P M<0Z!*Q$M@4M[!I QP)_'V:2*A,Y)L"X J901@ M,!#_:C$*P01B=@%L$"$Q8]=/Z/]?%4>";"9+>D4"%@:]%82# ^4U@;B=%H2/63#-E MTAPPK2ZP.B&Q(,!S?:%L*H%=>'=&"8 $D"6A1R=R;L]YHWW"`9!',&%YAK*- M@?UC,V9B`4"%.:%A8"MC(^3^)P0@+8$@L4@12/)M'TV1?R%A3# H-( _@4^" M7Q^C3_\NL#]V*F @P"*G,#"#L"U _W8`7R$P,!R@/#%V8Y67(,!+7'(%L&<` M<&EZ2R,Z+S2,2_(>("[ :6&Q("C[*Y($D&U^43^02!$$D4UR_R=Q3A0_@4=! M9F$NL ,@`U+3)+%3PF]J!9!T0(4A,3\`<"7S,#!<&WP6PA/%L$#04JZ,HK#Q,@?\OL5IQ,G$NL 01H-(.<%AA M_UQQE1\H83 P6",I,K!D$H'?I^ N,%]P*Y&A`RVN(IUOOCN'AC5V*\(_0#91 M=7U0Z4?S/RDT=DD_D"!25J'Q(H!$=5 "(9-B1S,\8_M< AH% _\6/Q`C T^._>H(1A.6%6$48(8"/02R.OFU$\<#1V'G Q+Y%R M1V'?`- &`"00">"C]D)&`>)R!$U!+' P,C$Q-"U A5 A<(V2-MCP+3.R-N<0 M-SGG<$<1="B0?0'0,HZVD*#FV@X@0(5%WBTFD ,0C;"$0&V(<=\AWD"$4N&3 M`A#B%BXY$4"%@F@"0' Z+R]W[: N+NM?[&L;P0#P``,`$! ``````P`1$ `` M``! ```#T``0````$``````````P`- '-/TW``!F14+H ` end From chemistry-request@www.ccl.net Thu Sep 17 18:07:26 1998 Received: from cz2.chem.niu.edu (cz2.chem.niu.edu [131.156.9.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id SAA23789 Thu, 17 Sep 1998 18:07:25 -0400 (EDT) Received: from cz.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/920502.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA03867; Thu, 17 Sep 98 16:11:10 -0500 Received: from smb.chem.niu.edu by cz.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA12851; Thu, 17 Sep 98 17:16:37 -0500 Received: from smb by smb.chem.niu.edu via SMTP (940816.SGI.8.6.9/940406.SGI) for id RAA05793; Thu, 17 Sep 1998 17:04:26 -0500 Sender: smb@smb.chem.niu.edu Message-Id: <36018769.59E2@smb.chem.niu.edu> Date: Thu, 17 Sep 1998 17:04:25 -0500 From: Steven Bachrach X-Mailer: Mozilla 3.01 (X11; I; IRIX 5.3 IP12) Mime-Version: 1.0 To: computational chemistry list Subject: ECCC5 Deadline for Abstracts Approaching Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Deadline for receipt of abstracts for the Fifth Electronic Computational Chemistry Conference (ECCC5) is FRIDAY, SEPTEMBER 25, 1998. ECCC5 is an online conference covering all aspects of computational chemistry. Articles are distributed using the web. Discussions are provided using a web-based interface. There is no registration fee for ECCC5. Complete information on the conference, including the form for submitting the abstract, can be found at http://hackberry.chem.niu.edu/ECCC5/ Please contact me if you have any questions or concerns. Steve -- Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From chemistry-request@www.ccl.net Thu Sep 17 22:01:51 1998 Received: from csb0.IPC.PKU.EDU.CN (csb0.ipc.pku.edu.cn [162.105.177.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id WAA24903 Thu, 17 Sep 1998 22:01:45 -0400 (EDT) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA13230; Fri, 18 Sep 98 09:58:12 -0700 Date: Fri, 18 Sep 1998 09:58:10 -0700 (PDT) From: Fenglou Mao To: Fabio Luiz Laurenti Garbujo Cc: chemistry@www.ccl.net Subject: Re: CCL:plot xyz In-Reply-To: <35FECF4A.DC23BDC6@lqt.dq.ufscar.br> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII gOpenMol see CCL ftp server. Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Peking University BeiJing P.R.China Tel:86-10-62751490 Fax:86-10-62751725