From walter@came.sbg.ac.at Fri Jul 4 03:49:46 1997 Received: from Agnes.came.sbg.ac.at for walter@came.sbg.ac.at by www.ccl.net (8.8.3/950822.1) id DAA18183; Fri, 4 Jul 1997 03:25:55 -0400 (EDT) Received: from Agnes (localhost [127.0.0.1]) by Agnes.came.sbg.ac.at (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id JAA13277 for ; Fri, 4 Jul 1997 09:25:13 +0200 Sender: walter@came.sbg.ac.at Message-ID: <33BCA559.15FB@came.sbg.ac.at> Date: Fri, 04 Jul 1997 09:25:13 +0200 From: Walter Koppensteiner Organization: Center for Applied Molecular Engineering X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: CCL Subject: Biological class libraries Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, I'm looking for class libraries to represent structure and/or sequence of a protein (and other biopolymers) in an object oriented way. C++ as the programming language is prefered but implementations in other OO languages are also welcome. Thanks in advance, Walter -- =============================================================== Walter Koppensteiner University of Salzburg Center of Applied Molecular Engineering Jakob Haringer Strasse 3 Phone: +43-662-8044-5794 A-5020 Salzburg, Austria Email: walter@came.sbg.ac.at =============================================================== From msj@fskru5.hre.hydro.com Fri Jul 4 05:49:46 1997 Received: from fskru5.hre.hydro.com for msj@fskru5.hre.hydro.com by www.ccl.net (8.8.3/950822.1) id FAA18789; Fri, 4 Jul 1997 05:14:55 -0400 (EDT) Received: by fskru5.hre.hydro.com (950413.SGI.8.6.12/930416.SGI.AUTO) for chemistry@www.ccl.net id MAA08109; Fri, 4 Jul 1997 12:14:06 +0200 From: "Merethe Sjovoll" Message-Id: <9707041214.ZM8107@fskru5.hre.hydro.com> Date: Fri, 4 Jul 1997 12:14:04 -0600 Reply-To: Merethe.Sjovoll@hre.hydro.com X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: QCPE Extended Hueckel Program (No. 571) Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello everyone, I was wondering whether anybody have experience with the QCPE program no. 571 which is an extended Hueckel program. I have certain problems when trying to run the test examples that follow the code. It appears that there is something wrong with the file that the EH code passes on to the property code (fort.1), although the EH calculation seem to run nicely. The program starts to read read the file, but the numbers are totally crazy. The other thing is the plotting program which follows, compiles with a lot of errors on an IBM 590. The README file that follows says the code is not debugged for SGI computers. It appears not to be for IBM either. Has anybody experienced the problems that I describe? Has anybody debugged the plotting program, and is it a big job? I would also be interested in having the programs run on an SGI machine. Please send eventual responses directly to me, as this subject is possibly of limited interest to most of the CClist members. Best wishes Merethe -- ******************************************************** Merethe Sjovoll, Ph.D. * * Research Scientist * * Norsk Hydro a.s Research Center * * * * P.O.Box 2560 * HYDRO * N-3901 Porsgrunn, * RESEARCH * Norway * * * ((( * email: Merethe.Sjovoll@hre.hydro.com * (=====) * Phone:+47 35 56 48 97 * * Fax :+47 35 56 36 86 * * ******************************************************** From jsl@virgil.ruc.dk Fri Jul 4 05:55:03 1997 Received: from emma.ruc.dk for jsl@virgil.ruc.dk by www.ccl.net (8.8.3/950822.1) id FAA18772; Fri, 4 Jul 1997 05:08:14 -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 LAA12720; Fri, 4 Jul 1997 11:13:51 +0200 (MET DST) Received: from VIRGIL/MAILQUEUE by virgil.ruc.dk (Mercury 1.21); 4 Jul 97 11:06:05 +0100 Received: from MAILQUEUE by VIRGIL (Mercury 1.21); 4 Jul 97 11:06:00 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: Dale Andrew Braden Date: Fri, 4 Jul 1997 11:06:00 +0100 Subject: Re: G: Gaussian Frequency calculation CC: chemistry@www.ccl.net Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <622060676B@virgil.ruc.dk> Dale: On 2 Jul 1997, you wrote: 07:36:12 -0700 (PDT) > If you get a response to this question, please post it to the CCL or G; I > am very interested in hearing the answer, as I have wondered about the > validity of Rupert's claim myself. I don't understand why people write > their own routines to diagonalize the full force-constant matrix provided > by G94, when it would be much simpler to just mass-weight the > eigenvectors, and renormalize. As you may have gathered from the postings on the G-list, the discussion is continuing. It turns out that the 'proper' cartesian displacement coefficients are obtained from the printed G94 normal mode coefficients in the following way: MULTIPLY THE PRINTED G94 NORMAL MODE COEFFICIENTS BY THE INVERSE SQUARE ROOT OF THE REDUCED MASS 'M'. This produces the cartesian displacement vector X in 'real' x-space, that corresponds to a normal mode vector Q of unit length in abstract, mass-weighted q-space. It is as simple as that, and you have the following relation between the length of the two vectors: |Q| = sqr(M)|X|. This, of course, should be well known by a lot of people (?), but I had to find it out by myself. John Bertie has recently worked it all out in formal matrix algebra. Another problem: You suggest a posting on the CCL, but my recent attempts to submit messages to CCL have been without effect: I get no mail error messages, but my messages don't appear on the list! What may be wrong? I am out of town for the next two weeks. Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= 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 page@plains.NoDak.edu Thu Jul 3 12:19 EDT 1997 Received: from plains.NoDak.edu for page@plains.NoDak.edu by bedrock.ccl.net (8.8.6/950822.1) id MAA15827; Thu, 3 Jul 1997 12:19:00 -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 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 Content-Type: text/plain; charset="us-ascii" Content-Length: 2602 Status: RO --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 Bernard.B.Pirard@GBJHA.zeneca.com Thu Jun 26 12:00 EDT 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 1\ 2:00:55 -0400 (EDT) Relayed; Thu, 26 Jun 1997 16:59:58 +0100 Thu, 26 Jun 1997 17:24:44 +0100 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 Dear colleagues, Acouple of days ago, I posted a query on AMBER parameters and charges. Thanks to all of you who have replied. Please find enclosed a summary of the replies. Sincerely Bernard Pirard Computational Chemistry Group Zeneca Agrochemicals Jealott’s Hill Bracknell Berkshire UK Bernard.B.Pirard@GBJHA.zeneca.com Bernard Pirard of Zeneca inquired about the availability of AMBER parameters for treating generic organic molecules. The primary reference for the "official" AMBER force field is: CORNELL WD; CIEPLAK P; BAYLY CI; GOULD IR; and others. A SECOND GENERATION FORCE FIELD FOR THE SIMULATION OF PROTEINS, NUCLEIC ACIDS, AND ORGANIC MOLECULES. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995 MAY 17, V117 N19:5179-5197. The set of parameters described therein represents a complete set for modelling proteins and nucleic acids containing standard residues. The force field is also described as being appropriate for organic molecules, however, the set of parameters available for modelling such molecules is far from complete. When studying the interactions between small molecules and proteins or nucleic acids, bonded parameters can often be borrowed from other force fields. Charges for a new molecule, however, need to be calculated from an ab initio generated HF/6-31G* wave function using the RESP protocol as described in these references: BAYLY CI; CIEPLAK P; CORNELL WD; KOLLMAN PA. A WELL-BEHAVED ELECTROSTATIC POTENTIAL BASED METHOD USING CHARGE RESTRAINTS FOR DERIVING ATOMIC CHARGES - THE RESP MODEL. JOURNAL OF PHYSICAL CHEMISTRY, 1993 OCT 7, V97 N40:10269-10280. CORNELL WD; CIEPLAK P; BAYLY CI; KOLLMAN PA. APPLICATION OF RESP CHARGES TO CALCULATE CONFORMATIONAL ENERGIES, HYDROGEN BOND ENERGIES, AND FREE ENERGIES OF SOLVATION. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1993 OCT 20, V115 N21:9620-9631. Variations of the AMBER force field have been implemented in various modelling packages and typically include the bonded and VDW parameters but use charges derived using a simpler and less costly approach. These implementations may be quite useful but it should be noted that they differ from the original force field. The "bona fide" AMBER force field was optimized to perform well at calculating relative energies of interaction in solution rather than, for example, screening large sets of compounds in a DOCKing procedure. For those who want to carry out MD studies in solution involving functional groups for which parameters are not available in the JACS reference, members of the Kollman research group as well as other members of the AMBER community often have derived such parameters. We are currently working on developing additional parameters, however, it will still fall to the user to calculate charges for a new molecule. Cheers, =Wendy Cornell _________________________________________________________________________________ Wendy D. Cornell, Ph.D. Senior Scientist Biomolecular Structure and Drug Design Chemistry Parke-Davis Research Ann Arbor, MI 48105 USA Bernard, If you have AMBER parameters for a particular cofactor or inhibitor, it may be easier to use them with Force Field Engine (FFE) in 6.3, rather than the original Kollman force field implementation in SYBYL. Let me know if you need documentation describing how to do this. Regards, Randy We have an AMBER program suite, and the force fields are referenced by authors. For example, the latest force field is the Cornell et al. version. See the AMBER web page for more detailed information, and to get the parameters. This version is optimized for liquid simulations- be aware that some programs still use our old parameters optimized for simulation in vacuum. http://www.amber.ucsf.edu/amber/ff94.html Regards Carlos From ahocquet@tamarugo.cec.uchile.cl Mon Jun 30 18:25 EDT 1997 Received: from tamarugo.cec.uchile.cl for ahocquet@tamarugo.cec.uchile.cl by www.ccl.net (8.8.3/950822.1) id SAA28759; Mon, 30 Jun 1997 18:24:53 -0400 (EDT) Received: from 146.83.5.131 ([146.83.10.67]) by tamarugo.cec.uchile.cl (5.0/SMI-SVR4(Thom)) id AA08407; Mon, 30 Jun 1997 18:27:52 +0400 Date: Mon, 30 Jun 1997 18:27:52 +0400 Message-Id: <9706302227.AA08407@tamarugo.cec.uchile.cl> X-Sender: ahocquet@tamarugo.cec.uchile.cl X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 To: chemistry@www.ccl.net From: Alexandre Hocquet Subject: semantics : a summary Content-Type: text/plain; charset="us-ascii" Content-Length: 6407 Status: R 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 From ahocquet@tamarugo.cec.uchile.cl Mon Jun 30 18:25 EDT 1997 Received: from tamarugo.cec.uchile.cl for ahocquet@tamarugo.cec.uchile.cl by www.ccl.net (8.8.3/950822.1) id SAA28762; Mon, 30 Jun 1997 18:25:16 -0400 (EDT) Received: from [146.83.10.67] by tamarugo.cec.uchile.cl (5.0/SMI-SVR4(Thom)) id AB08407; Mon, 30 Jun 1997 18:27:55 +0400 Date: Mon, 30 Jun 1997 18:27:55 +0400 Message-Id: <9706302227.AB08407@tamarugo.cec.uchile.cl> X-Sender: ahocquet@tamarugo.cec.uchile.cl X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 To: chemistry@www.ccl.net From: Alexandre Hocquet Subject: French computational chemistry ? Content-Type: text/plain; charset="us-ascii" 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 lestaw.k.bieniasz@uni-tuebingen.de Mon Jun 30 10:42 EDT 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 KAA24924; Mon, 30 Jun 1997 10:42:14 -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 AA00890; Mon, 30 Jun 97 16:41:46 MES Date: Mon, 30 Jun 1997 16:41:19 +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 Content-Length: 3365 Status: RO 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 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? 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 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... Status: RO Content-Length: 384 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 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 | | | ------------------------------------------------------- From gostowskir@apsu01.apsu.edu Mon Jun 30 08:49:02 1997 Received: from apsu02.apsu.edu for gostowskir@apsu01.apsu.edu by www.ccl.net (8.8.3/950822.1) id IAA23569; Mon, 30 Jun 1997 08:19:59 -0400 (EDT) Received: from gostowskir.apsu.edu by APSU02.APSU.EDU (PMDF V5.1-4 #16785) with ESMTP id <01IKOBJNMT5S0000VI@APSU02.APSU.EDU> for chemistry@www.ccl.net; Mon, 30 Jun 1997 07:18:27 CST Date: Mon, 30 Jun 1997 07:19:59 -0500 From: Rudy Gostowski Subject: molecular dynamics of anisotropic free radicals To: CCL group Message-id: <01IKOBJNNBN60000VI@APSU02.APSU.EDU> MIME-version: 1.0 X-Mailer: Microsoft Internet Mail 4.70.1155 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal CCL Group, I would like to do molecular dynamics calculations of anisotropic free radicals combining in a bimolecular fashion to form dimers. The reactants are sterically hindered carbon free radicals. Please suggest references and programs. I have read Solc & Stockmayer (1971). thanks, Rudy Rudy Gostowski Department of Chemistry Austin Peay State University Box 4547 Clarksville, TN 37044 615-648-7624 FAX 615-648-5996 gostowskir@apsu01.apsu.edu From rahsjc@rohmhaas.com Mon Jun 30 16:49:02 1997 Received: from nmho05u.rohmhaas.com for rahsjc@rohmhaas.com by www.ccl.net (8.8.3/950822.1) id QAA27784; Mon, 30 Jun 1997 16:33:02 -0400 (EDT) Received: by nmho05u.rohmhaas.com; id QAA29722; Mon, 30 Jun 1997 16:47:23 -0400 (EDT) Received: from fermi.sh.rohmhaas.com(136.141.248.15) by nmho05u.rohmhaas.com via smap (V3.1.1) id xma029644; Mon, 30 Jun 97 16:47:06 -0400 Received: from localhost (rahsjc@localhost) by fermi.sh.rohmhaas.com (AIX4.2/UCB 8.7/8.7) with SMTP id QAA44340; Mon, 30 Jun 1997 16:33:00 -0400 (EDT) X-Authentication-Warning: fermi.sh.rohmhaas.com: rahsjc owned process doing -bs Date: Mon, 30 Jun 1997 16:33:00 -0400 (EDT) From: "Subhas J. Chakravorty" X-Sender: rahsjc@fermi.sh.rohmhaas.com To: Shubin Liu cc: chemistry Subject: Re: CCL:calculate exchange energy from Hartree-Fock wavefunction In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The definition of exchange energy in the Roothaan Hartree Fock method (Open Shell is a multideterminantal wavefunction) is "unambiguosly:" defined As V(Ex)= Vee - Vcoul. V(coul) = 1/2 Integral [ (rho(1) Rho(2) ] Dt1 Dt2 if Lowdin definition that Hartree Fock doesnt contain correlation energy is used. Most of the coupling coeeficients are made so that only K survives At least in Prof. Gulzari Malli's tables. The other choice is to unravel Sasaki's code or look at Froese Fischers program. Therefore the Exchange energy contains, a little correlation energy implicit in the ROHF wavefunction for open shells. With an ROHF wavefunction it is hard to seperate Exchange and correlation. just as we cant in a CI wavefunction. ********************************************* In some cases though one can construct a single determinantal function for an open shell case using the ROHF orbitals. Then calculate using the UHF equations to determine exchange, since the total energy for the UHF and the ROHF is the same, only the UHF energy need not be at a minimum with the ROHF orbitals. ByeBye. On Mon, 30 Jun 1997, Shubin Liu wrote: > > Hi, All: > > I recently hope to calculate explicitly the exchange energy of atoms from > the restricted Hartree-Fock wavefunction of Clementi and Roetti. I > obtained the right answer from atoms with 1s and 2s orbitals, but found > something wrong for those with 2p or other orbitals. I guess it may be > related to my incorrect treatment of spherical harmonic polynomials when > l>=1. Can anyone point out how to do that? Thank a lot! > > Shubin > ............................................................................. Subhas J. Chakravorty, sjchakravorty@rohmhaas.com (215)-619-5481 Rohm and Haas Company Spring House, PA-19447 ************************************************************************** Disclaimer : Opinions in the above text are not of Rohm and Haas Company + ************************************************************************** From tcg@chem.unipune.ernet.in Tue Jul 1 02:49:07 1997 Received: from sangam.ncst.ernet.in for tcg@chem.unipune.ernet.in by www.ccl.net (8.8.3/950822.1) id CAA29847; Tue, 1 Jul 1997 02:11:58 -0400 (EDT) Received: from iucaa (iucaa.ernet.in [144.16.31.4]) by sangam.ncst.ernet.in (8.7.5) with SMTP id LAA19946 for ; Tue, 1 Jul 1997 11:48:46 +0530 (GMT+05:30) Received: from unipune.ernet.in by iucaa (5.65v3.2/SMI-4.1) id AA29914; Tue, 1 Jul 1997 11:38:17 +0500 Received: from chem.unipune.ernet.in by unipune.ernet.in (8.8.5/UNIPUNE-MAILHUB(02.04.97)) id LAA27533; Tue, 1 Jul 1997 11:37:24 -0500 (GMT) Received: by chem.unipune.ernet.in (8.7.5/SMI-SVR4) id LAA03100; Tue, 1 Jul 1997 11:48:40 -0500 Date: Tue, 1 Jul 1997 11:48:40 -0500 From: tcg@chem.unipune.ernet.in (Students of Dr. S.R. Gadre) Subject: Need Hammett sigma consts for dbly subs benzenes Message-Id: <199707011648.LAA03100@chem.unipune.ernet.in> To: CHEMISTRY@www.ccl.net Dear Sirs: We are looking for the observed Hammett sigma constants for doubly substituted benzenes involving NH2, NO2, CH3, Cl, OCH3 (ortho and meta). Kindly send us these values or suggest a suitable reference. Thank you ........................Shridhar R. Gadre From ccl@www.ccl.net Wed Jul 2 05:49:18 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id FAA06164; Wed, 2 Jul 1997 05:28:01 -0400 (EDT) Received: from destille.chemie.de for claessen@chemie.de by bedrock.ccl.net (8.8.6/950822.1) id FAA10875; Wed, 2 Jul 1997 05:28:00 -0400 (EDT) Received: by destille.chemie.de (Smail3.2.0.90) from claessen (132.187.248.147) with smtp id ; Wed, 2 Jul 1997 11:27:28 +0200 (MET DST) Message-Id: Comments: Authenticated sender is From: "Rolf Claessen" Organization: University of Wuerzburg, Dept. of Chemistry To: chemistry@ccl.net Date: Wed, 2 Jul 1997 11:25:40 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Winners of "Top 5% Chemistry Site" Award!! Reply-to: s101264@stud-mail.uni-wuerzburg.de Priority: normal X-mailer: Pegasus Mail for Win32 (v2.52) Winners of "Top 5% Chemistry Site" Award!! The Homepage for Chemists http://www-public.rz.uni-duesseldorf.de/~knecht/chempage.htm and Rolf Claessen's Chemistry Index http://www.geocities.com/Tokyo/5243/award_en.htm announce the winners of the "Top 5% Chemistry Site" - Award, wich honours the best 5% of the applications. The award is given to pages that are chemistry related, highly informative, make use of the latest technology and are easy to explore. Yours sincerely, Rolf Claessen From yubofan@guomai.sh.cn Wed Jul 2 22:49:27 1997 Received: from gm-email.guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id WAA11150; Wed, 2 Jul 1997 22:35:42 -0400 (EDT) Received: from ------ (proxy01.visionet.com.au [210.0.0.17]) by gm-email.guomai.sh.cn (8.8.5/8.8.5) with ESMTP id LAA07040 for ; Thu, 3 Jul 1997 11:31:53 +0800 Message-Id: <199707030331.LAA07040@gm-email.guomai.sh.cn> From: "Yubo Fan" To: Subject: Want a program to control CPU time. Date: Thu, 3 Jul 1997 10:34:40 +0800 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1161 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, everyone, I use G94W to calculate some molecular systems on my PC. My OS is Windows 95. When the calculations are running, all CPU time is used by this software and I cannot run other software easily. Is there a program which can allocate a part of time to a certain program, for instance, the program can allocate 90% CPU time to G94W and other software can use another 10% resourses? If there is one, please tell me. I really need it. Thank you very much Y. FAN =================================================== FAN, Yubo Department of Chemistry Fudan University Shanghai, 200433 P. R. China Voice(86-21)65492222-4294 =================================================== From ccl@www.ccl.net Wed Jul 2 23:49:28 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id XAA11263; Wed, 2 Jul 1997 23:03:07 -0400 (EDT) Received: from mmlds1.pha.unc.edu for iiv@mmlds1.pha.unc.edu by bedrock.ccl.net (8.8.6/950822.1) id XAA03174; Wed, 2 Jul 1997 23:03:06 -0400 (EDT) Received: by mmlds1.pha.unc.edu (5.57/TAS/11-16-88) id AA22533; Wed, 2 Jul 97 23:19:06 -0400 Newsgroups: bionet.molec-model,bionet.biology.computational Date: Wed, 2 Jul 1997 23:18:50 -0400 (EDT) From: Iosif Vaisman To: CCL Subject: ACS Course in Molecular Modeling Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The American Chemical Society Short Course Molecular Modeling, Computational/Combinatorial Chemistry, and Chemical Diversity : Methods and Techniques August 19-22, 1997 Laboratory for Molecular Graphics and Theoretical Modeling College of Pharmacy, University of Texas at Austin The introductory course will be especially valuable for experimental chemists who design drugs or carry out syntheses, as well as other R&D scientists in the organic, medicinal, or biochemical fields. Each student will have their own Silicon Graphics workstation and access to desktop computers for the duration of the short course. There will be daily "hands-on" laboratory sessions so YOU can work with state-of-the-art hardware and software. Topics: Molecular Mechanics Calculations, Molecular Mechanics Parameterization, Quantum Mechanics Calculations, Conformational Searching, Drug Design, Pharmacophore Development, 3D Databases, 3D Searching Strategies, and Combinatorial Chemistry Concepts Who Should Attend? Anyone wanting to know more about molecular structure calculations, pharmacophore design, 3D database searching, and structure-function relationships. The course has been designed primarily for experimental scientists in industry or academics with a background in the chemical, biological, and/or biomedical sciences. Software: MM2/MM3, SYBYL, INSIGHT/DISCOVER, QUANTA/CHARMm, SPARTAN, ISIS, CONCORD, CAChe, and more Lecturers J. Phillip Bowen (University of Georgia) Norman L. Allinger (University of Georgia) Alex Tropsha (University of North Carolina) Warren Hehre (Wavefunction, Inc.) Bob Pearlman (University of Texas at Austin) Osman Guner (MSI) Call the ACS Education Services/Short Course Office at (800) 227-5558 or (202) 872-4508 or FAX (202) 872-6336 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 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 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.