From Jeffrey.Gosper@brunel.ac.uk Thu Jul 3 06:03:38 1997 Received: from himiko.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.8.3/950822.1) id FAA12601; Thu, 3 Jul 1997 05:02:06 -0400 (EDT) Received: from castjjg.brunel.ac.uk (actually chem-pc-03.brunel.ac.uk) by himiko.brunel.ac.uk with SMTP-BRUNEL (PP); Thu, 3 Jul 1997 10:02:05 +0100 Date: Thu, 3 Jul 1997 09:58:45 PDT From: Jeffrey Gosper Subject: Windows interface to BABEL available To: CHEMISTRY@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear CCL users, we have completed a Windows interface for BABEL (a popular and free chemistry file conversion program - versions 1.06 and 1.6 for DOS) that we are making available to the Chemistry community. It is a general utility and may be regarded as a 'tag-on' program for Re_View, although you don't need Re_View to enjoy its functinality. BABELwin allows the user to select the file input/output types/filenames and then runs the DOS version of BABEL in a DOS shell (as such the user must have BABEL installed on their computer). We find that the Windows interface greatly increases the rate at which we can develop files for MOPAC (using a molecular editor to create a PDB file and converting this to a MOPAC input file) and also conversion MOPAC and other QM packagess output so it can graphically viewed. If you would like to obtain BABELwin then you can down load the 16 bit or 32 bit version from: ftp.brunel.ac.uk/pc/chem/babelw16.exe or babelwin.exe Please drop me an Email message when you download BABELwin. Also an comments and bug reports are welcomed. Further information on BABEL is available at: ftp://joplin.biosci.arizona.edu/pub/Babel/ /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper, Dept. of Chemistry, BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187, facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://www.brunel.ac.uk/~castjjg Re_View's home page (molecular animations or Chem-4D): http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From tcg@chem.unipune.ernet.in Thu Jul 3 06:49:33 1997 Received: from sangam.ncst.ernet.in for tcg@chem.unipune.ernet.in by www.ccl.net (8.8.3/950822.1) id GAA12795; Thu, 3 Jul 1997 06:16:14 -0400 (EDT) Received: from iucaa (iucaa.ernet.in [144.16.31.4]) by sangam.ncst.ernet.in (8.7.5) with SMTP id PAA14160 for ; Thu, 3 Jul 1997 15:52:28 +0530 (GMT+05:30) Received: from unipune.ernet.in by iucaa (5.65v3.2/SMI-4.1) id AA02407; Thu, 3 Jul 1997 15:41:42 +0500 Received: from chem.unipune.ernet.in by unipune.ernet.in (8.8.5/UNIPUNE-MAILHUB(02.04.97)) id PAA03955; Thu, 3 Jul 1997 15:40:47 -0500 (GMT) Received: by chem.unipune.ernet.in (8.7.5/SMI-SVR4) id WAA09183; Wed, 2 Jul 1997 22:56:52 -0500 Date: Wed, 2 Jul 1997 22:56:52 -0500 From: tcg@chem.unipune.ernet.in (Students of Dr. S.R. Gadre) Message-Id: <199707030356.WAA09183@chem.unipune.ernet.in> To: CHEMISTRY@www.ccl.net Subject: Hammett constants Dear Sirs: We are looking for the observed Hammett sigma constants for doubly substituted benzenes involving NH2, NO2, CH3, Cl, OCH3 (ortho and meta) sustituents. These are probably obtained from the 3,4- and 3,5- disubstituted benzoic acids. Kindly send us these values or suggest a suitable reference. Thank you ........................Shridhar R. Gadre From page@plains.NoDak.edu Thu Jul 3 12:49:38 1997 Received: from plains.NoDak.edu for page@plains.NoDak.edu by www.ccl.net (8.8.3/950822.1) id MAA14635; Thu, 3 Jul 1997 12:18:58 -0400 (EDT) Received: from [134.129.127.25] (p.chem.ndsu.NoDak.edu [134.129.127.25]) by plains.NoDak.edu (8.8.5/8.8.5) with SMTP id LAA16577; Thu, 3 Jul 1997 11:18:58 -0500 (CDT) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 3 Jul 1997 10:22:49 -0600 To: chemistry@www.ccl.net From: page@plains.NoDak.edu (Michael Page) Subject: ACS THEORY/IBM grad student computer awards - call for Apps. Cc: jkl@ccl.net --Call for Applicants IBM Graduate Student Awards in Computational Chemistry Below is an announcement for two Awards in Computational Chemistry that are open to current graduate students. We are grateful to IBM and the Minnesota Supercomputing Institute for their support of these awards. Let me urge you to encourage your graduate students to apply. The competition is open to any graduate student (regardless of citizenship) who began graduate study after August 1, 1994 and who is an ACS member (or whose advisor is an ACS member). These awards are designed to encourage graduate work in stimulate interest in the Subdivision of Theoretical Chemistry and the Physical Chemistry Division of the ACS. An Awards Committee will consider all the applicants. The awards applications should be sent to Professor Bill Hase at Wayne State University. Note that the deadline for applications is August 15. These two awards, supported by IBM, will provide one-time cash stipends of $2500 and $1000 as supplements to normal financial aid to doctoral candidates in the research-dissertation stage in the 1997-1998 academic year. The Minnesota Supercomputing Institute will provide each awardee up to 1000 node-hours on an IBM SP2 cluster for the awardees to actually carry out a portion of the awarded research. The awardees will have access to the consulting services of the Institute normally available to all users. Awardee selection will be made on a competitive basis. Applicants should be working on new and innovative computational chemistry methods or applications in theoretical chemistry. Applicants should prepare a written description of a computational chemistry research project that requires high performance computing, with an explanation of the scientific importance of the project. Proposals need to include an estimate of the computing resources required in SP2 cpu-hours. Applicants should explain how they plan to use the grant funds. Two letters of recommendation, including one from the student's advisor, along with a vita and transcript, are required. The proposal, including the vita, should not exceed five double-spaced pages. In addition, a faculty person (typically the applicant's research advisor) responsible for the applicant's use of the Minnesota Supercomputing Institute resources must be identified. Forward applications by August 15, 1997 to Prof. Bill Hase Department of Chemistry Wayne State University Detroit, MI 48202 hase@sun.chem.wayne.edu The awardees will be chosen and announced at the Fall 1997 ACS National Meeting. From jsl@virgil.ruc.dk Thu Jul 3 13:49:37 1997 Received: from emma.ruc.dk for jsl@virgil.ruc.dk by www.ccl.net (8.8.3/950822.1) id NAA15229; Thu, 3 Jul 1997 13:37:43 -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 TAA04603 for ; Thu, 3 Jul 1997 19:43:23 +0200 (MET DST) Received: from VIRGIL/MAILQUEUE by virgil.ruc.dk (Mercury 1.21); 3 Jul 97 19:35:38 +0100 Received: from MAILQUEUE by VIRGIL (Mercury 1.21); 3 Jul 97 19:35:34 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: chemistry@www.ccl.net Date: Thu, 3 Jul 1997 19:35:29 +0100 Subject: CCL: CC semantics Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <529E185716@virgil.ruc.dk> I sent this message a couple of times, but for some reason it did not appear on CCL: Statement by 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 burke@agouron.com Thu Jul 3 13:49:44 1997 Received: from tbone.agouron.com for burke@agouron.com by www.ccl.net (8.8.3/950822.1) id NAA15254; Thu, 3 Jul 1997 13:44:33 -0400 (EDT) Received: by tbone.agouron.com (951211.SGI.8.6.12.PATCH1042/951211.SGI) for <@tbone.agouron.com:CHEMISTRY@www.ccl.net> id KAA18084; Thu, 3 Jul 1997 10:44:41 -0700 Received: from relay(192.135.144.39) by tbone.agouron.com via smap (3.1) id xma018075; Thu, 3 Jul 97 10:44:36 -0700 Received: from cardinal by eggo via ESMTP (950215.SGI.8.6.10/951211.SGI) for <@tbone.agouron.com:CHEMISTRY@www.ccl.net> id KAA05933; Thu, 3 Jul 1997 10:44:34 -0700 Received: by cardinal (950215.SGI.8.6.10/951211.SGI) id KAA02032; Thu, 3 Jul 1997 10:44:33 -0700 From: "Ben Burke" Message-Id: <9707031044.ZM2030@cardinal.agouron.com> Date: Thu, 3 Jul 1997 10:44:32 -0700 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@www.ccl.net Subject: CCL: G92: SCF Convergence Problem: 6-31+G* Cc: burke@cardinal.agouron.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear G92-ers: I was unable to optimize two systems when I changed from the 6-31g* basis set to 6-31+g* basis set. The systems of interest are neutral and anionic heterocycles, containing C,O,N,H. I optimized the neutral species at the 6-31g* level (no +), and obtained the final geometry. I used this geometry (without a polar proton) as the starting point for the optimization of the anionic species. The SCF calculation for the anionic species would not converge under RHF or UHF conditions, even using the quadratic convergence option. I checked the wavefunction of the step prior to this one, and the wavefunction is stable. After these investigations with the anionic species, I tried to optimize the neutral species at the 6-31+g* level, and it failed. Has anyone seen anything like this before (something converges at 6-31G*, but fails at 6-31+G*)? I used G92 for the calculations, running on an SGI R8000, IRIX Release 6.1. A few details on the calculations are given below after a longer description. Any ideas what to try next? Of course, I will pass along a summary of the responses. Thanks, --Ben ------------------------------------------------------------------------- Long version with a few details folowing: ------------------------------------------------------------------------- I optimized a neutral heterocyclic structure at the 6-31g* level. (neutral) rhf/6-31g* E(RHF) = -680.159849444 A.U. I was interested in the properties of the anion (charge=-1). So, starting with the 6-31G* optimized structure, I removed an NH proton, and submitted a job for optimization at the 6-31+G* level. In the second step of the minimization, the SCF fails to converge. I tried to remediate (or evaluate) in several ways: 1. I repeated the run with scf=(novaracc) to maintain integral accuracy, but the job failed exactly as before. 2. I investigated the stability of the wavefunction in the prior step, and it showed no instabilities (see anion, run 2). 3. I tried the optimization with scf=qc, and a large scfcyc value in order to try to get convergence (see anion, run 3). 4. Although the energy separation seems adequate to make sure that there is spin-pairing, I ran the job using UHF in order to make sure that some di-radical is not be preferred. So far, there is no convergence after 1001 steps. When reviewing what I had done, I decided for completeness sake that I should try to optimize the neutral species using diffuse functions (6-31+g*). It failed! (1) rhf/6-31+g* E(RHF) = -680.134141544 A.U. E(RHF) = -686.040030921 A.U. --> Fails ------------------------------------------------------------------------- A few details on the submissions and consequent output ------------------------------------------------------------------------- ******** (anion, run 1a: Failed Run) ******** rhf/6-31+g* scf=direct opt test pop=full SCF Done: E(RHF) = -679.621506401 A.U. after 22 cycles Convg = 0.8071D-08 -V/T = 2.0031 S**2 = 0.0000 Copying SCF densities to generalized density rwf, ISCF=0 IROHF=0. .... >>>>>>>>>> Convergence criterion not met. SCF Done: E(RHF) = -684.524654296 A.U. after 65 cycles Convg = 0.8578D-03 -V/T = 2.0078 S**2 = 0.0000 Convergence failure -- run terminated. ******** (anion, run 2: Check Stability of Prior Step) ******** rhf/6-31+g* scf=(direct,novaracc) stable=opt test pop=none geom=check The wavefunction is stable under the perturbations considered. The wavefunction is already stable. E(RHF) = -679.621506401 ******** (anion, run 3: Optimize with Quadratic Convergence) ******** rhf/6-31+g* scf=(direct,novaracc,qc) opt scfcyc=1000 test pop=reg geom=check Iteration 96... The polynomial fit failed. Using point 1. A contracting polynomial of degree 16 produced 0.0000 Search did not lower the energy significantly. No lower point found -- run aborted. ******** (anion, run 4: Try with UHF) ******** uhf/6-31+g* scf=(direct,novaracc) opt scfcyc=1000 test pop=reg geom=check SCF Done: E(UHF) = -679.621506401 A.U. after 22 cycles >>>>>>>>>> Convergence criterion not met. SCF Done: E(UHF) = -684.550622760 A.U. after 1001 cycles Convg = 0.4300D+01 -V/T = 2.0078 S**2 = 0.0000 -- ---------------------------------------------------------------------- Benjamin J. Burke Agouron Pharmaceuticals burke@agouron.com Research Scientist 3565 General Atomics Ct Tel: (619) 622-3018 Computational Chemistry San Diego, CA 92121 FAX: (619) 622-3299 ---------------------------------------------------------------------- From tvolm@blue.weeg.uiowa.edu Thu Jul 3 14:49:37 1997 Received: from mail-hub1.weeg.uiowa.edu for tvolm@blue.weeg.uiowa.edu by www.ccl.net (8.8.3/950822.1) id OAA15762; Thu, 3 Jul 1997 14:17:47 -0400 (EDT) Received: from green.weeg.uiowa.edu (tvolm@green.weeg.uiowa.edu [128.255.56.25]) by mail-hub1.weeg.uiowa.edu (8.7.6/8.7.3) with ESMTP id NAA15042 for ; Thu, 3 Jul 1997 13:17:48 -0500 Received: from localhost by green.weeg.uiowa.edu (8.7.6/client-1.3) id NAA27846; Thu, 3 Jul 1997 13:17:48 -0500 Date: Thu, 3 Jul 1997 13:17:47 -0500 (CDT) From: volm timothy gerard X-Sender: tvolm@green.weeg.uiowa.edu To: chemistry@www.ccl.net Subject: Unsubscribe Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Unsubscribe From ccl@www.ccl.net Thu Jul 3 16:49:38 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id QAA16585; Thu, 3 Jul 1997 16:00:01 -0400 (EDT) Received: from plato.chem.iupui.edu for morreale@chem.iupui.edu by bedrock.ccl.net (8.8.6/950822.1) id PAA21839; Thu, 3 Jul 1997 15:59:58 -0400 (EDT) Received: from localhost by plato.chem.iupui.edu (940816.SGI.8.6.9/MSU-2.04) id UAA10701; Thu, 3 Jul 1997 20:17:07 GMT Date: Thu, 3 Jul 1997 15:17:07 -0500 (EST) From: Antonio Morreale To: chemistry@ccl.net Subject: Probe atom in CoMFA Sybyl Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, In Sybyl, The CoMFA steric field is computed with a carbon sp3 atom. By default this probe atom has a +1 charge, and I wonder why?. A positively charged probe makes sense for an electrostatic probe, but why is a +1 necessary for the steric field probe?. Thanks. Antonio. From ahocquet@tamarugo.cec.uchile.cl Thu Jul 3 20:49:40 1997 Received: from ariane.ens-cachan.fr for ahocquet@tamarugo.cec.uchile.cl by www.ccl.net (8.8.3/950822.1) id UAA17201; Thu, 3 Jul 1997 20:37:34 -0400 (EDT) Received: from nemo.rip.ens-cachan.fr (root@nemo.rip.ens-cachan.fr [138.231.46.2]) by ariane.ens-cachan.fr (8.8.5/jtpda-5.1) with ESMTP id CAA16520 for ; Fri, 4 Jul 1997 02:37:35 +0200 (MET DST) Received: from nemo.rip.ens-cachan.fr ([146.83.10.67]) by nemo.rip.ens-cachan.fr (8.8.5/jtpda-5.2) with SMTP id CAA07524 for ; Fri, 4 Jul 1997 02:36:29 +0200 (MET DST) Date: Fri, 4 Jul 1997 02:36:29 +0200 (MET DST) Message-Id: <199707040036.CAA07524@nemo.rip.ens-cachan.fr> X-Sender: hocquet@nemo.rip.ens-cachan.fr 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 ahocquet@tamarugo.cec.uchile.cl Thu Jul 3 20:49:46 1997 Received: from ariane.ens-cachan.fr for ahocquet@tamarugo.cec.uchile.cl by www.ccl.net (8.8.3/950822.1) id UAA17197; Thu, 3 Jul 1997 20:36:52 -0400 (EDT) Received: from nemo.rip.ens-cachan.fr (root@nemo.rip.ens-cachan.fr [138.231.46.2]) by ariane.ens-cachan.fr (8.8.5/jtpda-5.1) with ESMTP id CAA16516 for ; Fri, 4 Jul 1997 02:36:52 +0200 (MET DST) Received: from nemo.rip.ens-cachan.fr ([146.83.10.67]) by nemo.rip.ens-cachan.fr (8.8.5/jtpda-5.2) with SMTP id CAA07518 for ; Fri, 4 Jul 1997 02:35:40 +0200 (MET DST) Date: Fri, 4 Jul 1997 02:35:40 +0200 (MET DST) Message-Id: <199707040035.CAA07518@nemo.rip.ens-cachan.fr> X-Sender: hocquet@nemo.rip.ens-cachan.fr 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