From ccl@www.ccl.net Fri Jun 27 03:58:56 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id DAA08806; Fri, 27 Jun 1997 03:11:47 -0400 (EDT) Received: from fecit-gate.fecit.co.uk for nobes@fecit.co.uk by bedrock.ccl.net (8.8.6/950822.1) id DAA24679; Fri, 27 Jun 1997 03:11:45 -0400 (EDT) Received: by fecit-gate.fecit.co.uk; id JAA13344; Fri, 27 Jun 1997 09:10:29 +0100 (BST) Received: from suisei.fecit.co.uk(192.168.101.50) by fecit-gate.fecit.co.uk via smap (V3.1.1) id xma013342; Fri, 27 Jun 97 09:10:09 +0100 Received: (from nobes@localhost) by suisei.fecit.co.uk (8.6.9/8.6.9) id IAA06178; Fri, 27 Jun 1997 08:13:53 +0100 From: Ross Nobes Message-Id: <199706270713.IAA06178@suisei.fecit.co.uk> Subject: Re: CCL:MOLZYME? To: toukie@zui.unizh.ch (Hr. Dr. S. Shapiro) Date: Fri, 27 Jun 1997 08:13:53 +0100 (BST) Cc: chemistry@ccl.net In-Reply-To: <1.5.4.32.19970622144043.0066676c@highdent.zzmk.unizh.ch> from "Hr. Dr. S. Shapiro" at Jun 22, 97 04:40:43 pm X-Mailer: ELM [version 2.4 PL25] Content-Type: text Hr. Dr. S. Shapiro writes: > > Has anyone ever heard of a programme called (someting like) MOLZYME? > I've heard that this is a modified version of MOPAC which is supposed to be > able to handle macromolecules, but I've been unable to find out anything > about it. > MOZYME is a semiempirical molecular orbital program written by James J.P. Stewart and marketed through Fujitsu. It uses localized molecular orbitals to overcome the N^3 diagonalization bottleneck of conventional programs like MOPAC. It is aimed at small proteins and enzymes of up to about 20,000 atoms. You can get further information about MOZYME at the following URL: http://iti2.net:80/jstewart/mozdesc.htm Regards, Ross Nobes -- +---------------------------------------------------------------------+ | Dr Ross Nobes | | Research Manager | | Fujitsu European Centre for Information Technology | | 2 Longwalk Road Phone: +44 (0)468 684 335 | | Stockley Park Fax: +44 (0)181 606 4422 | | Uxbridge UB11 1AB, UK E-mail: nobes@fecit.co.uk | +---------------------------------------------------------------------+ From Herve.TOULHOAT@ifp.fr Fri Jun 27 04:03:53 1997 Received: from ifp.ifp.fr for Herve.TOULHOAT@ifp.fr by www.ccl.net (8.8.3/950822.1) id DAA08903; Fri, 27 Jun 1997 03:45:16 -0400 (EDT) Received: from irsil47.ifp.fr(156.118.20.167) by ifp.ifp.fr via smap (1.3.1) id sma023694; Fri, 27 Jun 97 09:31:32 MET DST From: "Herve Toulhoat" Message-Id: <9706270930.ZM3340@irsil47> Date: Fri, 27 Jun 1997 09:30:56 -0600 In-Reply-To: "Hr. Dr. S. Shapiro" "CCL:MOLZYME?" (Jun 22, 4:40pm) References: <1.5.4.32.19970622144043.0066676c@highdent.zzmk.unizh.ch> X-Mailer: Z-Mail (3.2.1 6apr95 MediaMail) To: "Hr. Dr. S. Shapiro" , chemistry@www.ccl.net Subject: Re: CCL:MOLZYME? Cc: nobes@fecit.co.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Jun 22, 4:40pm, Hr. Dr. S. Shapiro wrote: > Subject: CCL:MOLZYME? > > > Dear Colleagues; > > Has anyone ever heard of a programme called (someting like) MOLZYME? > I've heard that this is a modified version of MOPAC which is supposed to be > able to handle macromolecules, but I've been unable to find out anything > about it. > > Thanks in advance to all responders. > > > Sincerely, > > S. Shapiro > toukie@zui.unizh.ch > > > > --- > 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 > --- >-- End of excerpt from Hr. Dr. S. Shapiro To my knowledge, MOLZYME is curently under development by Fujitsu. Try to contact Dr Ross NOBES: +---------------------------------------------------------------------+ | Dr Ross Nobes | | Research Manager | | Fujitsu European Centre for Information Technology | | 2 Longwalk Road Phone: +44 (0)468 684 335 | | Stockley Park Fax: +44 (0)181 606 4422 | | Uxbridge UB11 1AB, UK E-mail: nobes@fecit.co.uk | +---------------------------------------------------------------------+ Yours sincerely, -- ---------------------------------------------------------------------------- Dr HERVE TOULHOAT Group Leader Molecular Modeling and Computational Chemistry Div. Computer Science and Applied Mathematics INSTITUT FRANCAIS DU PETROLE Tel: +33-01-47-52-73-50 1 & 4 Avenue de Bois-Preau Fax: +33-01-47-52-70-22 BP 311 92852 RUEIL-MALMAISON Cedex FRANCE E-mail: herve.toulhoat@ifp.fr ---------------------------------------------------------------------------- From ahocquet@tamarugo.cec.uchile.cl Fri Jun 27 05:48:17 1997 Received: from tamarugo.cec.uchile.cl for ahocquet@tamarugo.cec.uchile.cl by www.ccl.net (8.8.3/950822.1) id EAA09243; Fri, 27 Jun 1997 04:51:50 -0400 (EDT) Received: from 146.83.5.131 ([146.83.10.67]) by tamarugo.cec.uchile.cl (5.0/SMI-SVR4(Thom)) id AA22617; Fri, 27 Jun 1997 04:53:47 +0400 Date: Fri, 27 Jun 1997 04:53:47 +0400 Message-Id: <9706270853.AA22617@tamarugo.cec.uchile.cl> X-Sender: ahocquet@tamarugo.cec.uchile.cl 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: Alexandre Hocquet Subject: French computational chemistry ? Dear CClers, this message has been posted in French because of its local interest. You will find a short translation into frenglish at the end. Chers CCLeurs, Suite aux messages de semantique sur la modelisation moleculaire et la "chimie computationnelle", j'aimerais faire un petit recensement parmi les CCLeurs de France, pour savoir qui se definit comme un "computational chemist". Sauf erreur, cette expression n'existe pas en francais et la lecture recente des comptes rendus 1996 de situation des sections 16 et 17 du cnrs me laisse penser qu'il existe en France : -des chimistes theoriciens (clairement en section 17) -des biophysiciens (sections 20,21 ?), mais aucune ASSOCIATION de CHIMISTES "computationnels" (voir les definitions et la distinction avec la chimie theorique dans Reviews in Computational Chemistry, Vol 1, page vii) Si vous pensez etre plus qu'un utilisateur occasionnel des techniques de la "chimie computationnelle", mais si vous ne vous definissez ni comme un chimiste theoricien, ni comme un biophysiscien, je serais tres heureux de recevoir votre reponse . Je ferais un resume si il y a suffisament d'interet. Due to the fact that "computationnal chemistry" does not exist in the french language as it seems that no "computational chemist" community has been formed in France, i intend to make a census of whoever considers himself as a computational chemist and works in France. If you're not french but want to comment on this, you are welcome. Alexandre Hocquet Facultad de Ciencias Fisicas Universidad de Chile Blanco Encalada, 2008 Santiago Centro CHILE fono : 56 2 678 45 19 fax : 56 2 696 73 59 From jsl@virgil.ruc.dk Fri Jun 27 07:48:18 1997 Received: from emma.ruc.dk for jsl@virgil.ruc.dk by www.ccl.net (8.8.3/950822.1) id HAA09999; Fri, 27 Jun 1997 07:43:29 -0400 (EDT) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by emma.ruc.dk (8.8.5/8.8.5) with ESMTP id NAA05082; Fri, 27 Jun 1997 13:48:45 +0200 (MET DST) Received: from VIRGIL/MAILQUEUE by virgil.ruc.dk (Mercury 1.21); 27 Jun 97 13:41:42 +0100 Received: from MAILQUEUE by VIRGIL (Mercury 1.21); 27 Jun 97 13:41:32 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: Date: Fri, 27 Jun 1997 13:41:28 +0100 Subject: Re: CCL:CC semantics CC: chemistry@www.ccl.net Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <332891C47AF@virgil.ruc.dk> Buyong Ma, 23 Jun 1997: > We all know that computational chemistry is a young discipline ... I disagree. To me, computational chemistry started around 1800 with Dalton's law of multiple proportions, Gay-Lussac's law of relative volumes of reacting gases, etc. Indeed, the latter chemist stated almost two centuries ago: "We are perhaps not far removed from the time when we shall be able to submit the bulk of chemical phenomena to calculation" (J.L. Gay-Lussac, 1808) And Charles Babbage, the "Father of the Computer": "All of chemistry, and with it crystallography, would become a branch of mathematical analysis which, like astronomy, taking its constants from observation, would enable us to predict the character of any new compound and possibly the source from which its formation might be anticipated" (Ch. Babbage, 1838) At the time of these writers computational chemistry was little more than a dream, but Babbage's vision is uncannily precise in its predictions! Evidently, the concept of computational chemistry is as old as the history of modern chemistry. Jems >--< Quotes from T J O'Donnell http://www.eecs.uic.edu/~tj/quotes.html#computational_chemistry =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Department of Chemistry Phone: +45 46757781 + 2710 Roskilde University (RUC) Fax: +45 46757721 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://frederik.ruc.dk/dis/chem/psos =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From ccl@www.ccl.net Fri Jun 27 09:48:18 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id JAA10711; Fri, 27 Jun 1997 09:45:28 -0400 (EDT) Received: from europe.std.com for jle@world.std.com by bedrock.ccl.net (8.8.6/950822.1) id JAA00493; Fri, 27 Jun 1997 09:45:28 -0400 (EDT) Received: from world.std.com by europe.std.com (8.7.6/BZS-8-1.0) id JAA13193; Fri, 27 Jun 1997 09:45:28 -0400 (EDT) Received: by world.std.com (5.65c/Spike-2.0) id AA14968; Fri, 27 Jun 1997 09:45:27 -0400 Date: Fri, 27 Jun 1997 09:45:27 -0400 From: jle@world.std.com (Joe M Leonard) Message-Id: <199706271345.AA14968@world.std.com> To: chemistry@ccl.net Subject: MMFF atom typing question... Folks, Looking at the Merck Molecular FF articles (J Comp Chem 17,490(1996)), I am confused by the NPYL atom type. IN the Supplementary Material, this is called a pyrrole-like N, but the table on P. 507 only indicates TWO bound atoms, rather than the three in pyrrole... Am I missing something, or is this a type in the table? Thanks in advance! Joe Leonard jle@world.std.com From lestaw.k.bieniasz@uni-tuebingen.de Fri Jun 27 09:59:17 1997 Received: from outmail.zdv.uni-tuebingen.de for lestaw.k.bieniasz@uni-tuebingen.de by www.ccl.net (8.8.3/950822.1) id JAA10503; Fri, 27 Jun 1997 09:11:01 -0400 (EDT) Received: from echem5.orgchemie.chemie (echem5.orgchemie.chemie.uni-tuebingen.de) by outmail.zdv.uni-tuebingen.de (4.1/ZDV-Uni-Tuebingen-1.0) id AA00364; Fri, 27 Jun 97 15:10:38 MES Date: Fri, 27 Jun 1997 15:10:06 +0200 (W. Europe Daylight Time) From: "Lestaw K. Bieniasz" To: chemistry@www.ccl.net Subject: Re: CCL:CC semantics Message-Id: X-X-Sender: coibi01@mailserv.uni-tuebingen.de Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Tuebingen, 27.06.97 Dear Dr. Buyong Ma, Yes, you're right I posted that letter a couple of months ago, but there were not too many responses. (Nevertheless, I wish to thank to those who responded). My personal point of view (unfortunately not shared with the scientific establishment) is that we should not pay too much attention to the classification of scientific activities. It should not really matter whether somebody is doing chemistry or physics or physical chemistry, etc. The only thing that matters should be the quality of the research. I wish we all could say "we do science", instead of trying hard to specify which particular part of it we do. I am sure this attitude would bring more progress into science, since it would allow the individuals to freely cross the real or imaginary borders between various research areas. This way of looking at science would also remove some of the semantic difficulties that you mention. But of course this is an idealistic dream, since in reality everything in science is divided into disciplines, and this system is very conservative, although as you rightly point out, there is a lot of overlapping between the disciplines (often viewed as uncomfortable). Now, since it looks that we indeed have to live in this reality, then my suggestion simply is that we use right words to denote things. Thus, in my opinion the term "computational chemistry" should be used to denote what it (literally) means. And it certainly means a combination of chemistry and computations, without specifying whether the subject is molecular or not. This understanding of computational chemistry is in a certain contrast to the current practice, in which the term "computational chemistry" is often interpreted in a much narrower sense, so that if my suggestion is accepted, it would indeed mean a certain enlargement of the scope of the (currently understood) computational chemistry. Note, however, that I have not invented this "new" definition, because it is already contained in one of the volumes of "Reviews in Computational Chemistry" ! In the same spirit, I think that the term "molecular modelling" should be used to denote any kind of modelling in which the assumed molecular structure of matter plays a central role, independently of whether the modelling is computational or not, although in practice it will of course be mostly computational, because non-computational methods are of limited use here. With best regards, Yours sincerely, L.Bieniasz *-------------------------------------------------------------------* | Dr. Leslaw Bieniasz | | temporary address: (3rd April 1997 - 31st August 1997) | | Institut fuer Organische Chemie, Universitaet Tuebingen | | Auf der Morgenstelle 18, 72076 Tuebingen, Germany. | | E-mail: lestaw.k.bieniasz@uni-tuebingen.de | *-------------------------------------------------------------------* | permanent address: | | Institute of Physical Chemistry of the Polish Academy of Sciences,| | Molten Salts Laboratory, ul. Zagrody 13, 30-318 Cracow, Poland. | | E-mail: nbbienia@cyf-kr.edu.pl | *-------------------------------------------------------------------* From lestaw.k.bieniasz@uni-tuebingen.de Fri Jun 27 11:11:22 1997 Received: from outmail.zdv.uni-tuebingen.de for lestaw.k.bieniasz@uni-tuebingen.de by www.ccl.net (8.8.3/950822.1) id KAA10815; Fri, 27 Jun 1997 10:02:30 -0400 (EDT) Received: from echem5.orgchemie.chemie (echem5.orgchemie.chemie.uni-tuebingen.de) by outmail.zdv.uni-tuebingen.de (4.1/ZDV-Uni-Tuebingen-1.0) id AA00829; Fri, 27 Jun 97 16:01:47 MES Date: Fri, 27 Jun 1997 16:01:11 +0200 (W. Europe Daylight Time) From: "Lestaw K. Bieniasz" To: Prem Yadav Cc: chemistry@www.ccl.net Subject: Re: CCL:CC semantics/reply to Bieniasz In-Reply-To: <199706231617.MAA00426@www.ccl.net> Message-Id: X-X-Sender: coibi01@mailserv.uni-tuebingen.de Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Tuebingen, 27.06.97 Dear Dr. Yadav, Well, I may be right or wrong, or most likely the truth lies in-between. Anyway, I understand from your arguments that you belong to this group of scientists who prefer to place strong dividing lines between various scientific disciplines (you view computers and computations as nothing but tools to solve chemical problems). This is exactly opposite to the point of view I am trying to develop, since I would prefer to remove the artificial borders between the traditional scientific disciplines. Let me ask a question: If somebody elaborates a purely numerical algorithm of solving a particular type of a Schroedinger equation, that makes sense only in some chemical context, so that the method is not likely to be used outside, is he doing chemistry or computer science? Is he merely creating a new tool, or improving the chemical knowledge/methodology? (Is a methodology of solving problems in a scientific discipline a part of this discipline, or it's a quite separate matter?) If you say that it is only tool, then why do you actually see a need for "computational chemistry"? Wouldn't it be easier to say that there is only "chemistry" and that some people use computers as tools to solve chemical problems? But if you see a need for "computational chemistry", then isn't it perhaps that some new quality is created by joining the two fields (chemistry and computational science) together, that is not contained in none of the two areas separately? If so, then maybe you should not classify computers and computational methods merely as tools? What is a difference between computer modelling and simulation? I would agree to using both of them, and I doubt if there exist a single definition of "simulation" that would satisfy everybody. There was quite a funny article about this in one of early volumes of the journal called "Simulation" about 10-15 years ago. The name of the author was Fritz, as far as I remember (but I can be wrong), I would recommend this article to you and to everybody who likes to use the term "simulation" ... Best regards, L. Bieniasz *-------------------------------------------------------------------* | Dr. Leslaw Bieniasz | | temporary address: (3rd April 1997 - 31st August 1997) | | Institut fuer Organische Chemie, Universitaet Tuebingen | | Auf der Morgenstelle 18, 72076 Tuebingen, Germany. | | E-mail: lestaw.k.bieniasz@uni-tuebingen.de | *-------------------------------------------------------------------* | permanent address: | | Institute of Physical Chemistry of the Polish Academy of Sciences,| | Molten Salts Laboratory, ul. Zagrody 13, 30-318 Cracow, Poland. | | E-mail: nbbienia@cyf-kr.edu.pl | *-------------------------------------------------------------------* From vkitzing@sunny.mpimf-heidelberg.mpg.de Fri Jun 27 11:52:18 1997 Received: from otto.mpimf-heidelberg.mpg.de for vkitzing@sunny.mpimf-heidelberg.mpg.de by www.ccl.net (8.8.3/950822.1) id LAA11932; Fri, 27 Jun 1997 11:34:50 -0400 (EDT) Received: from sunny.mpimf-Heidelberg.mpg.de by otto.mpimf-heidelberg.mpg.de (4.1/SMI-4.1) id AA02207; Fri, 27 Jun 97 17:34:40 +0200 Received: from [149.217.50.47] (mac20) by sunny.mpimf-Heidelberg.mpg.de (4.1/SMI-4.1) id AA01594; Fri, 27 Jun 97 17:31:18 +0200 X-Sender: vkitzing@sunny.MPImF-Heidelberg.mpg.de (Unverified) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 27 Jun 1997 17:30:20 +0200 To: "Hr. Dr. S. Shapiro" , chemistry@www.ccl.net From: vkitzing@sunny.mpimf-heidelberg.mpg.de (Eberhard von Kitzing) Subject: Re: CCL:van der Waals radii for amino acids Cc: toukie@zui.unizh.ch Dear Prof. Shapiro, At 16:01 Uhr 24.06.1997, Hr. Dr. S. Shapiro wrote: > For a calculation I wish to perform, I require the van der Waals >radii of each of the atoms (including hydrogen) in the 20 common amino >acids. If anyone can recommend a published source of this information (or >if anyone should happen to have this information as an e-mailable file), >I would appreciate hearing from you. Of course the list of relevant articles is very long. Below please consider a small subset. -------------------------------------------------------- Misako Aida, Giorgina Corongiu and Enrico Clementi (1992). "Ab Initio force fields for simulations of proteins and nucleic acids." International Journal of Quantum Chemistry 42 1353-1381. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, et al. (1995). "A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules." Journal of the American Chemical Society 117(19) 5179-5197. T. P. Creamer and G. D. Rose (1995). "Simple force-field for study of peptide and protein conformational properties." Methods in Enzymology 259 576-589. P. Derreumaux and G. Vergoten (1995). "A new spectroscopic molecular mechanics force-field - parameters for proteins." Journal of Chemical Physics 102(21) 8586-8605. David M. Ferguson and Peter A. Kollman (1991). "Can the Lennard-Jones 6-12 Function Replace the 10-12 Form in Molecular Mechanics Calculations." Journal of Computational Chemistry 12(5) 620-626. Thomas A. Halgren (1992). "Representation of van der Waals (vdW) Interactions in Molecular Mechanics Force Fields: Potential Form, Combination Rules, and vdW Parameters." Journal of the American Chemical Society 114 7827-7843. T. A. Halgren (1996). "Merck molecular-force field .2. mmff94 van-der-waals and electrostatic parameters for intermolecular interactions." Journal of Computational Chemistry 17(5-6) 520-552. M.J. Hwang, T. Stockfisch, M. Hassan, D. Nguyen and A.T. Hagler (1993). "Class-ii force-fields for peptides and proteins ." Biophysical Journal 64(N2) A 12-12. William L. Jorgensen and Julian Tirado-Rives (1988). "The OPLS Potential Functions for Proteins. Energy Minimizations for Crystalls of Cyclic Peptides and Crambin." Journal of the American Chemical Society 110(6) 1657. M. Kroeker and H. J. Lindner (1996). "The pimm force-field - recent developments." Journal of Molecular Modeling 2(9) 376-378. Jenn-Huei Lii and Norman L. Allinger (1991). "The MM3 Force Field for Amides, Polypeptides and Proteins." Journal of Computational Chemistry 12(2) 186-199. G. Luiti and F. Pirani (1985). "Regularities in van-der-Waals forces: Correlations between the potential parameters and polarizability." Chemical Physics Letters 122(3) 245-250. K. T. No, O. Y. Kwon, S. Y. Kim, K. H. Cho, C. N. Yoon, Y. K. Kang, K. D. Gibson, M. S. Jhon and H. A. Scheraga (1995). "Determination of nonbonded potential parameters for peptides." Journal of Physical Chemistry 99(34) 13019-13027. A. K. Rappe, C. J. Casewit, K. S. Colwell, W. A. Goddard III and W. M. Skiff (1992). "UFF, a Full periodic tabel Force Field for molecular mechanics and molecular dynamics simulation." Journal of the American Chemical Society 114 10024-10035. Scott J. Weiner, Peter A. Kollman, David A. Case, U. Chandra Singh, Caterina Ghio, Giuliano Alagona, Savatore Jr. Profeta and Paul Weiner (1984). "A New Force Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins." Journal of the American Chemical Society 106 765-784. ====================================================================== Eberhard von Kitzing Max-Planck-Institut fuer Medizinische Forschung Jahnstr. 29 D 69115 Heidelberg Germanny email: vkitzing@sunny.mpimf-heidelberg.mpg.de WWW: http://sunny.mpimf-heidelberg.mpg.de/people/vkitzing/Eberhard.html From buyong@ibmnla.chem.uga.edu Fri Jun 27 12:48:21 1997 Received: from dns1.uga.edu for buyong@ibmnla.chem.uga.edu by www.ccl.net (8.8.3/950822.1) id MAA12529; Fri, 27 Jun 1997 12:21:37 -0400 (EDT) From: Received: from ibmnla.chem.uga.edu (ibmnla.chem.uga.edu [128.192.5.8]) by dns1.uga.edu (8.8.5/8.8.3) with SMTP id MAA29244 for ; Fri, 27 Jun 1997 12:21:41 -0400 Received: from localhost by ibmnla.chem.uga.edu (AIX 3.2/UCB 5.64/4.03) id AA19927; Fri, 27 Jun 1997 12:21:27 -0400 Date: Fri, 27 Jun 1997 12:21:26 -0400 (EDT) To: chemistry@www.ccl.net Subject: Re: CCL:CC semantics In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Tuebingen, 22.06.97 Dear Dr. Buyong Ma, Yes, you're right I posted that letter a couple of months ago, but there were not too many responses. (Nevertheless, I wish to thank to those who responded). My personal point of view (unfortunately not shared with the scientific establishment) is that we should not pay too much attention to the classification of scientific activities. It should not really matter whether somebody is doing chemistry or physics or physical chemistry, etc. The only thing that matters should be the quality of the research. I wish we all could say "we do science", instead of trying hard to specify which particular part of it we do. I am sure this attitude would bring more progress into science, since it would allow the individuals to freely cross the real or imaginary borders between various research areas. This way of looking at science would also remove some of the semantic difficulties that you mention. But of course this is an idealistic dream, since in reality everything in science is divided into disciplines, and this system is very conservative, although as you rightly point out, there is a lot of overlapping between the disciplines (often viewed as uncomfortable). Now, since it looks that we indeed have to live in this reality, then my suggestion simply is that we use right words to denote things. Thus, in my opinion the term "computational chemistry" should be used to denote what it (literally) means. And it certainly means a combination of chemistry and computations, without specifying whether the subject is molecular or not. This understanding of computational chemistry is in a certain contrast to the current practice, in which the term "computational chemistry" is often interpreted in a much narrower sense, so that if my suggestion is accepted, it would indeed mean a certain enlargement of the scope of the (currently understood) computational chemistry. Note, however, that I have not invented this "new" definition, because it is already contained in one of the volumes of "Reviews in Computational Chemistry" ! In the same spirit, I think that the term "molecular modelling" should be used to denote any kind of modelling in which the assumed molecular structure of matter plays a central role, independently of whether the modelling is computational or not, although in practice it will of course be mostly computational, because non-computational methods are of limited use here. With best regards, Yours sincerely, L.Bieniasz *-------------------------------------------------------------------* | Dr. Leslaw Bieniasz | | temporary address: (3rd April 1997 - 31st August 1997) | | Institut fuer Organische Chemie, Universitaet Tuebingen | | Auf der Morgenstelle 18, 72076 Tuebingen, Germany. | | E-mail: lestaw.k.bieniasz@uni-tuebingen.de | *-------------------------------------------------------------------* | permanent address: | | Institute of Physical Chemistry of the Polish Academy of Sciences,| | Molten Salts Laboratory, ul. Zagrody 13, 30-318 Cracow, Poland. | | E-mail: nbbienia@cyf-kr.edu.pl | *------------------------------------------------------------------- From bradley@mail.enterprise.net Fri Jun 27 15:48:28 1997 Received: from dns0.enterprise.net for bradley@mail.enterprise.net by www.ccl.net (8.8.3/950822.1) id OAA13892; Fri, 27 Jun 1997 14:49:01 -0400 (EDT) Received: from default (ppp424.enterprise.net [194.72.196.170]) by dns0.enterprise.net (8.8.5/8.7.3) with SMTP id TAA18917; Fri, 27 Jun 1997 19:51:56 +0100 (BST) Message-Id: <199706271851.TAA18917@dns0.enterprise.net> Comments: Authenticated sender is From: "David Bradley Science Writer" To: "Randy Zauhar" Date: Fri, 27 Jun 1997 19:50:51 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:Nanomodels Reply-to: Bradley@enterprise.net CC: CHEMISTRY@www.ccl.net Priority: urgent In-reply-to: <9706271004.ZM6427@xhost4.tripos.com> References: "David Bradley Science Writer" "CCL:Nanomodels" (Jun 23, 8:30am) X-mailer: Pegasus Mail for Win32 (v2.53/R1) > David, > > Could you post pointers to the nanotech. software packages you > mentioned? http://www.digitalspace.com/papers/nanopap1.html for AMOEBA http://www.carol.com/mass.shtml for MASS http://world.std.com/~wware.ncad.html for NanoCAD Look out for my paper in SCW in September 1997 Dave Bradley ------------------------------------------------------- | David Bradley Science Writer | | Bradley@enterprise.net | | Tel/Fax +44 1223 440834 | | | | Elemental Discoveries: chemical happenings on the web | | http://homepages.enterprise.net/bradley/elem1.html | | | -------------------------------------------------------