From Bernard.B.Pirard@GBJHA.zeneca.com Thu Jun 26 12:48:10 1997 Received: from bath.mail.pipex.net for Bernard.B.Pirard@GBJHA.zeneca.com by www.ccl.net (8.8.3/950822.1) id MAA05324; Thu, 26 Jun 1997 12:00:55 -0400 (EDT) X400-Received: by mta bath.mail.pipex.net in /PRMD=pipex/ADMD=pipex/C=gb/; Relayed; Thu, 26 Jun 1997 16:59:58 +0100 X400-Received: by /PRMD=ZENECA/ADMD=PIPEX/C=GB/; Relayed; Thu, 26 Jun 1997 17:24:44 +0100 Date: Thu, 26 Jun 1997 17:24:44 +0100 X400-Originator: Bernard.B.Pirard@GBJHA.zeneca.com X400-Recipients: chemistry@www.ccl.net X400-MTS-Identifier: [/PRMD=ZENECA/ADMD=TMAILUK/C=GB/;970626162444] Original-Encoded-Information-Types: ia5-text X400-Content-Type: P2-1984 (2) Content-Identifier: CSI NC V3.0 From: Pirard Bernard B Message-ID: <0016BC5E.MAI*/I=B/G=Bernard/S=Pirard/OU=GBJHA/PRMD=ZENECA/ADMD=PIPEX/C=GB/@MHS> To: cclq Subject: amber parameters and charges; summary MIME-version: 1.0 Content-type: multipart/mixed; boundary="oBUKVKmipynCFXjIOHiqdkAaYdvC6pop" 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//////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////w== --oBUKVKmipynCFXjIOHiqdkAaYdvC6pop-- From ahocquet@tamarugo.cec.uchile.cl Thu Jun 26 20:48:14 1997 Received: from tamarugo.cec.uchile.cl for ahocquet@tamarugo.cec.uchile.cl by www.ccl.net (8.8.3/950822.1) id UAA07723; Thu, 26 Jun 1997 20:46:30 -0400 (EDT) Received: from 146.83.5.131 ([146.83.10.67]) by tamarugo.cec.uchile.cl (5.0/SMI-SVR4(Thom)) id AA10925; Thu, 26 Jun 1997 20:47:46 +0400 Date: Thu, 26 Jun 1997 20:47:46 +0400 Message-Id: <9706270047.AA10925@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: semantics : a summary Dear CCLers, I have recently posted a message regarding the different possible interpretations of the expression "molecular modelling" in the CCL community. Thanks to all who replied. The answers seemed to converge on the fact that two different common interpretations may be understood (as defined in my original posting) and that the "classical methods" definition originates in that part of the "community" involved with drug design, biomolecular modelling, etc... Quite surprinsingly, the debate that followed focused on definitions of "computational chemistry", a theme that has been already discussed (again see original message). Anyway, be it computational chemistry or molecular modelling, it appears that everyone has his definition, depending on what computational chemistry (or what molecular modelling) he is involved in. Should this situation linger on, as a proof that computational chemistry is interdisciplinary , or do we need something like a iupac definition (as apparently such a thing does not exist) ? Well, i guess this is another discussion... By the way, thanks to Georg Schrekenbach for his spelling enlightment. Both spellings seem acceptable... The original message : Dear CCLers, While Boyd and Lipkowitz once intended to review definitions of "computational chemistry" (Reviews in Computational Chemistry, Vol 1, page vii), the words "molecular modelling" still appear confusing to me : While it seems logical to think that "molecular modelling" is that part of "computational chemistry" that describes behaviour of molecules by the formalism of some theoretical model, there seems to exist in the community a much more restrictive use of "molecular modelling". This second definition could be "Use of any non quantum mechanics model to describe the behaviour of molecules". If one looks at the scope of the Journal of Molecular Modeling, no semi empirical, ab initio, dft methods are quoted, while the general guidelines state that "The Journal of Molecular Modeling will cover all aspects of computational chemistry". Another example, the ICCCRE XII congress divides the scientific program in different topics. Amongst them : - Semi empirical and Ab initio quantum chemistry, dft methods - Molecular Modeling, QSAR Any hints on a proper definition ? Any historical reason for different uses of "molecular modelling" ? And, above all, one or two l ? The replies that did not appear directly in the CCL : Alexandre , In my humble opinion the term "molecular modelling" is indeed confusing at best, i think that in most circumstances the term is used where "molecular mechanics" would be better - i.e. solving classical equations of motion. (and both can be abrieviated to "MM") noj -- Dr. Noj Malcolm Theory Group, Dept. of Chemistry, University of Manchester, Oxford Road, Manchester. M13 9PL Yo estoy de acuerdo con la definicion que das antes, son tecnicas de quimica computacional que permiten simular o medelar sistemas moleculares a travez de formulismo de modelos teoricos, yo pienso que no se restringen exclusivamente a metodos no-QM, lo que pasa es que en general se atribuye el termino de modelado molecular a tecnicas usadas en biomoleculas o en macromoleculas en general, y con tal cantidad de atomos quedan descartado los metodos de QM, si se quieres analizar todo esa macromolecula... en todo caso hay varios trabajos que mezclan tenicas de dinamica molecular y de QM, primero estudiando las conformaciones de la macromolecula con DM y luego en un entorno mas especifico, el sitio activo (con mucho menos atomos), con QM. La otra tecnica que creo que ha cobrado gran interes son los metodos hibridos QM/MM, en dosnde se definen zonas QM y zonas MM, se mezclan los Hamiltonianos de las zonas QM con los Potenciales de MM, y "ojo" que no se tienen malos resultados en cuanto a calculos de delta G, y otras energias. En resumen, el molecular modelling, a mi juicio, no esta restringido estrictamente a metodos no-QM, sino que a todos los metodos para simulacion de sistemas macromoleculares, especilemente de interes biologico, tal vez por la estrecha relacion que existe entre molecular modelling y "molecular desing", de gran interes en la industrias Farmaceuticas Espero que te ayuda en algo esto, nos vemos en algun congreso! Danilo Gonzalez. Universidad de Santiago de Chile Facultad de Quimica y Biologia http://quimbio.usach.cl/~danilo/ Hi Alexandre, this sounds like an interesting question so a summary in the CCL would be appreciated. I have seen both of your definitions with the second one being more often used (to increase confusion, you can also add "simulation" vs. "modelling" ...). One more little comment >And, above all, one or two l ? My dictionary (Langenscheidt English - German) doesn't contain "model(l)ing", however, for "model(l)er" both one and two l are offered without any preference. Regards, Georg You raise an interesting point. > Any hints on a proper definition ? For some reason, "molecular modeling" is usually used to encompass non-quantum-mechanical treatments of chemical structures. In common usage, it tends to refer to molecular mechanics as well as pure visualization, and to things "in between", such as rule-based methods for docking and hand-manipulation of structures, generally on a computer. I really don't have any good idea why or how the term got to include these things and to exclude others, nor am I aware of any formal definition. Like your original comments, my sense of how the word is used is based on how I've seen the term used -- not on any formal definition I've seen. -P. -- **** "Deep Blue can't triumph in the game of life." (NY Times, 5/13/97) *** * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * 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