From chemistry-request@www.ccl.net Fri Nov 20 09:30:28 1998 Received: from glamdring.memphis.edu (glamdring.memphis.edu [141.225.223.241]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA14742 Fri, 20 Nov 1998 09:30:28 -0500 (EST) Received: from memphis.edu ([141.225.145.178]) by glamdring.memphis.edu (8.8.8/8.8.8) with ESMTP id IAA25935 for ; Fri, 20 Nov 1998 08:30:28 -0600 (CST) Message-ID: <36557D42.CC042513@memphis.edu> Date: Fri, 20 Nov 1998 08:31:30 -0600 From: Abby Parrill Organization: University of Memphis X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: 'Using Computers to Facilitate Learning' symposium, last call Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCL-ers, I would like to invite the contribution of a few more oral presentations to fill out a symposium for the ACS Meeting in Anaheim this spring entitled 'Using Computers to Facilitate Learning'. I am interested in contributions that discuss new learning tools, as well as those that discuss the use of computers to facilitate learning activities (where the computer is not necessarily providing content). This symposium is sponsored by the COMP division, and co-sponsored by the CHED division and the CHED Committee on Computers in Chemical Education (CCCE). The abstract deadline for this symposium was November 18th, but I will be accepting abstracts at least until the end of the day on Monday, November 23rd. If you are using computers to help students learn, please share your successes (and advice regarding problems!) with your colleagues through this symposium. Electronic submission of abstracts is preferred (the abstract form is available on the ACS website at www.acs.org). Regards, Abby _____________________________________________ Abby L. Parrill (901)678-2638 Assistant Professor (901)678-3447 Department of Chemistry University of Memphis Memphis, TN 38152 aparrill@memphis.edu Computational Research on Materials Institute at The University of Memphis (CROMIUM) _____________________________________________ From chemistry-request@www.ccl.net Fri Nov 20 09:46:45 1998 Received: from dirac.cnrs-orleans.fr (dirac.cnrs-orleans.fr [163.9.6.67]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA14871 Fri, 20 Nov 1998 09:46:16 -0500 (EST) Received: (from hinsen@localhost) by dirac.cnrs-orleans.fr (AIX4.3/UCB 8.8.8/8.7) id PAA20158; Fri, 20 Nov 1998 15:42:07 +0100 Date: Fri, 20 Nov 1998 15:42:07 +0100 Message-Id: <199811201442.PAA20158@dirac.cnrs-orleans.fr> X-Authentication-Warning: dirac.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: mkh100@york.ac.uk CC: chemistry@www.ccl.net In-reply-to: (message from Michael Hodgson on Thu, 19 Nov 1998 11:50:45 +0000 (GMT)) Subject: Re: CCL:Charmm DCD file format References: > Is there an easy way of converting DCD files between machine architectures > ? Here is one way to do it, using MMTK (see http://starship.skyport.net/crew/hinsen/mmtk.html). The recipe is: 1) Convert the DCD trajectory to an MMTK trajectory, which uses the portable netCDF format. This must be done on the machine where the DCD file was generated. 2) Copy the netCDF file to the machine where you want to use the data. 3) Convert the netCDF trajectory back to DCD. The disadvantege of this procedure is that you must have access to both types of machine. If the difference between the two Fortran binary file formats is just byte order, you might use a general tool for converting Fortran files. Morale: don't use non-portable file formats! -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@www.ccl.net Fri Nov 20 14:25:20 1998 Received: from deimos.cber.nih.gov (deimos.cber.nih.gov [128.231.52.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA17668 Fri, 20 Nov 1998 14:25:19 -0500 (EST) Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA180649791; Fri, 20 Nov 1998 14:23:11 -0500 Date: Fri, 20 Nov 1998 14:23:11 -0500 (EST) From: Rick Venable To: Konrad Hinsen Cc: mkh100@york.ac.uk, chemistry@www.ccl.net Subject: Re: CCL:Charmm DCD file format In-Reply-To: <199811201442.PAA20158@dirac.cnrs-orleans.fr> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Note that CHARMM provides this facility via an intermediate formatted file, created and decoded by the DYNAnmics FORMat/UNFOrmat commands, respectively. These utility commands have existed for well over the past decade or so, and were designed explicitly for this purpose. Of course, you need CHARMM on both machine types to do this as well. Moral: read the documentation On Fri, 20 Nov 1998, Konrad Hinsen wrote: > > Is there an easy way of converting DCD files between machine architectures > > ? > > Here is one way to do it, using MMTK (see > http://starship.skyport.net/crew/hinsen/mmtk.html). The recipe is: > > 1) Convert the DCD trajectory to an MMTK trajectory, which uses the > portable netCDF format. This must be done on the machine where > the DCD file was generated. > 2) Copy the netCDF file to the machine where you want to use the data. > 3) Convert the netCDF trajectory back to DCD. > > The disadvantege of this procedure is that you must have access to > both types of machine. If the difference between the two Fortran > binary file formats is just byte order, you might use a general tool > for converting Fortran files. > > Morale: don't use non-portable file formats! > -- > ------------------------------------------------------------------------------- > Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr > Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 > Rue Charles Sadron | Fax: +33-2.38.63.15.17 > 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ > France | Nederlands/Francais > ------------------------------------------------------------------------------- > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: chemistry-request@www.ccl.net > -- Original Sender From: Address: hinsen@cnrs-orleans.fr > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov | \ / |=| position of the FDA; for that, http://www.erols.com/rvenable \/ |=| see http://www.fda.gov ) From chemistry-request@www.ccl.net Fri Nov 20 16:19:54 1998 Received: from rrpac.upr.clu.edu (upracd.UPR.CLU.EDU [136.145.88.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id QAA18570 Fri, 20 Nov 1998 16:19:53 -0500 (EST) Received: from localhost by rrpac.upr.clu.edu (5.65v4.0/1.1.10.5/13Aug97-0135PM) id AA29697; Fri, 20 Nov 1998 17:19:53 -0400 Date: Fri, 20 Nov 1998 17:19:53 -0400 (GMT-0400) From: DANIEL BACELO To: chemistry@www.ccl.net Subject: fhi96md on SGI? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am looking where to find a copy for the program for periodic structures "fhi96md" to run in a SGI Thank you in advance Dr. Daniel Bacelo Dep. of Science and Technology Universidad Metropolitana P. O. Box 21150, San Juan, PR 00928-1150 Phone: (787)- 766-1717 ext 6117 Fax (787) 751-5386 email: daniel@pauli.uprr.pr From chemistry-request@www.ccl.net Thu Nov 19 07:32:25 1998 Received: from impact.dyn.unipg.it (impact.dyn.unipg.it [141.250.17.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA05505 Thu, 19 Nov 1998 07:32:20 -0500 (EST) Received: from vanadis.chm.unipg.it (vanadis.chm.unipg.it [141.250.9.71]) by impact.dyn.unipg.it (8.9.1a/8.9.1) with SMTP id NAA01635; Thu, 19 Nov 1998 13:10:22 +0100 (MET) Message-Id: <3.0.5.32.19981119130113.007e0100@impact.dyn.unipg.it> X-Sender: deneb@impact.dyn.unipg.it X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Thu, 19 Nov 1998 13:01:13 +0100 From: COMET XVI To:chemistry@www.ccl.net Subject: COMET XVI Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=====================_911473273==_" --=====================_911473273==_ Content-Type: text/plain; charset="us-ascii" --=====================_911473273==_ Content-Type: text/plain; charset="iso-8859-1" Content-Disposition: attachment; filename="mail.txt" Content-Transfer-Encoding: quoted-printable XVI INTERNATIONAL CONFERENCE ON MOLECULAR ENERGY TRANSFER COMET XVI June 20-25, 1999 "La Cittadella", Assisi, ITALY http://www.chm.unipg.it/chimgen/mb/cong/comet.html e-mail: comet@dyn.unipg.it ***********1st Announcement************ The XVI International Conference On Molecular Energy Transfer,=20 COMET XVI, will be held at "La Cittadella", a conference facility in Assisi, ITALY, 20-25 June 1999. Assisi is a unique medieval=20 town rich in art masterpieces. It is located in a beautiful=20 landscape, 25 km east of Perugia, the capital of the Umbria region known as the "green heart" of Italy. The COMET is a Gordon type=20 conference held every two years alternating between the USA and Europe. The purpose of the 1999 conference is to survey recent advances,=20 undertake stimulating discussions, generate new ideas, and map out=20 future directions in the field of molecular energy transfer. The scientific program will concentrate on dynamical aspects=20 of molecular energy transfer. Particular emphasis will be given to * State-to-state dynamics * Inelastic and reactive collisions * Unimolecular reactions=20 * Ion reaction dynamics * State-selected (inter- and intra-molecular) energy transfer * Internal vibrational redistribution * Energy transfer in condensed phase * Clusters and hydrogen bonded systems * Photodissociation * Imaging techniques * Non-adiabatic processes * Open-shell dynamics and spectroscopy * Transition state spectroscopy * Femtosecond dynamics INVITED SPEAKERS M.H. Alexander (University of Maryland) M.N.R. Ashfold (University of Bristol) G. Balint-Kurti (University of Bristol) J.M. Bowman (Emory University) D.C. Clary (University College London) F.F. Crim (University of Wisconsin) O. Dutuit (Universit=E8 de Paris-Sud, Orsay) G.R. Fleming (University of California, Berkeley) G.W. Flynn (Columbia University) D.R. Herschbach (Harvard University) F. Huisken (Max-Planck-Institut, G=F6ttingen) M.I. Lester (University of Pennsylvania) J.C. Light (University of Chicago) W.C. Lineberger (JILA, University of Colorado) K. Liu (IAMS, Academia Sinica, Taipei) H.H.J. ter Meulen (University of Nijmegen) W.H. Miller (University of California, Berkeley) E. Murad (Air Force Research Lab, Hanscom AFB) R. Naaman (Weizmann Institute, Rehovot) D. Nesbitt (JILA, University of Colorado) D.M. Neumark (University of California, Berkeley) G.A. Parker (University of Oklahoma) H. Reissler (University of Southern California) G. Scoles (Princeton University) J.P. Simons (Oxford University) T. Suzuki (IMS, Okazaki) F. Vecchiocattivi (University of Perugia) R.N. Zare (Stanford University) Chair: Piergiorgio Casavecchia, Co-Chair Dipartimento di Chimica Universit=E0 di Perugia 06123 Perugia, Italy Phone: (+39) (075) 585-5514 Fax: (+39) (075) 585-5606 Email: piero@dyn.unipg.it=20 Antonio Lagana`, Co-Chair Dipartimento di Chimica Universit=E0 di Perugia=09 06123 Perugia, Italy Phone: (+39) (075) 585-5515 Fax: (+39) (075) 585-5606 Email: lag@dyn.unipg.it The local organizing committee includes the members of the=20 Perugia Group: V. Aquilanti, N. Balucani, B. Brunetti,=20 R. Candori, D. Cappelletti, S. Cavalli, S. Crocchianti,=20 S. Falcinelli, G. Grossi, G. Liuti, E. Luzzatti, F. Pirani,=20 F. Vecchiocattivi, G.G. Volpi.=20 __________________________________________________________ Note that COMET XVI will be followed immediately after by=20 the "Workshop on Quantum Reactive Scattering" (Perugia, Italy,=20 25-27 June 1999) and by the 1st European Computational Chemistry School on "Molecular and Reaction Dynamics" (Perugia, Italy,=20 June 28-July 4, 1999).=20 _________________________________________________________ Information will be continuously updated on the Web site.=20 On January 1999 it will be e-mailed to people on the Conference=20 mailing list. To be added to the mailing list, please fill out=20 the form and mail or fax it. You can also pre-register at our=20 Web Site: http://www.chm.unipg.it/chimgen/mb/cong/comet.html The Second Announcement will include more specific details=20 about the call for papers, registration, fees, traveling=20 and housing. PRE-REGISTRATION FORM To receive further information, register at our WWW site=20 http://www.chm.unipg.it/chimgen/mb/cong/comet.html or return this slip (e-mail, fax, or regular mail) before January 15, 1999. Last Name:________________________________________ First Name:_______________________________________ E-mail:___________________________________________ =09 Phone:____________________________________________ Fax:______________________________________________ Address:__________________________________________ __________________________________________________ __________________________________________________ If you are unable to access our WWW site, please=20 check here ___ to receive a hard copy of forthcoming=20 information. COMET XVI Prof. P.Casavecchia Dipartimento di Chimica Universita` di Perugia Via Elce di Sotto, 8 06123 PERUGIA ITALY FAX: (39) 075 5855606 e-mail comet@dyn.unipg.it --=====================_911473273==_ Content-Type: text/plain; charset="us-ascii" ______________________________________________________________________ Nadia Balucani Tel.: (39) (075) 585 5513 Dipartimento di Chimica Fax: (39) (075) 585 5606 Universita` di Perugia e-mail: deneb@dyn.unipg.it Via Elce di Sotto, 8 www.chm.unipg.it/chimgen/mb/mb.html 06123 PERUGIA - ITALY --=====================_911473273==_-- From chemistry-request@www.ccl.net Thu Nov 19 08:54:33 1998 Received: from csb0.IPC.PKU.EDU.CN (csb0.ipc.pku.edu.cn [162.105.177.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id IAA05993 Thu, 19 Nov 1998 08:53:13 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA26878; Thu, 19 Nov 98 20:51:13 -0800 Date: Thu, 19 Nov 1998 20:51:12 -0800 (PST) From: Arthur Wang To: CCL mailing list Subject: Enhancing CoMFA: free program release Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, Comparative Molecular Field Analysis (CoMFA) has been widely used as a powerful 3D-QSAR tool in the field of medicinal chemistry since its birth in the late 1980s. It usually uses a grid to map the molecular field around the molecular aggregate and find out the relationship between the data on the grid and bioassay activities by PLS technique. However, several groups have reported that the orientation of the molecular aggregate has significant influence on the final result given by such a CoMFA procedure. Sometimes the q2 value in cross-validation may vary as much as 0.4 units among different orientations. We recently reported two enhanced sampling procedures, all-orientation search (AOS) and all-placement search (APS), for CoMFA analysis. According to AOS/APS, the molecular aggregate is rotated or translated systematically within the grid and a CoMFA is performed for each orientation or placement thus obtained. Among all the possible orientations or placements, the one yielding the highest q2 value is picked out. By such an exhaustive searching, the arbitrariness in the conventional CoMFA can be eliminated and the CoMFA result is therefore optimized. For more details about the method, please have a look at: Renxiao Wang, Ying Gao, Liang Liu, and Luhua Lai "All-Orientation Search and All-Placement Search in Comparative Molecular Field Analysis", Journal of Molecular Modeling, 4, 276-283. The program for performing AOS and APS is written in SYBYL/SPL script. A SYBYL user will find it very easy to run AOS and APS. The program is now available to the public. You can get it via anonymous FTP to ftp.ipc.pku.edu.cn (162.105.177.12) /pub/software/aos_aps/. Please forward this mail to whom may be concerned. Best wishes, Arthur _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Renxiao Wang Doctoral Candidate _/ _/ Molecular Design Laboratory _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-62751490 Fax: 86-10-62751725 _/ _/ WWW: http://www.ipc.pku.edu.cn/~arthur/arthur.html _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From chemistry-request@www.ccl.net Thu Nov 19 15:24:18 1998 Received: from njmsa.UMDNJ.EDU (root@njmsa.UMDNJ.EDU [130.219.34.100]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA09944 Thu, 19 Nov 1998 15:24:16 -0500 (EST) Received: from localhost (pyadav@localhost [127.0.0.1]) by njmsa.UMDNJ.EDU (8.8.6 (PHNE_14041)/8.8.6) with SMTP id PAA03362 for ; Thu, 19 Nov 1998 15:24:16 -0500 (EST) Date: Thu, 19 Nov 1998 15:24:16 -0500 (EST) From: Prem Yadav To: chemistry@www.ccl.net Subject: books on Mol.mod. & comp.chem. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, Following is the summary of my query about books in the area of molecular modeling, protein modeling, drug design and computational chemistry. I thank you all who responded to me. This really helped me in making my decission. Prem Yadav Molecular Mechanics Across Chemistry, by Rappe and Casewit (University Science Books, Sausalito, CA, 1997) Molecular Modelling: Principles and Applications, by Leach (Addison Wesley Longman, Essex UK, 1996). 1). Guidebook on Molecular modeling in Drug Design, edited by N. Claude Cohen, Academic Press 2). Computer Aided molecular design, Theory and applications, J. P. Doucet and J. weber, Academic Press 3). Exploring QSAR, Corwin Hansch and Albert Leo Computer-aided Molecular Design, Understanding Molecular Simulation, Molecular Modeling and Drug Design. Bioinformatics: the molecular modeling approach. > I have found the following to be most useful: > > 1. "Computational Chemistry", 1995, GH Grant and WG Richards, Oxford, > Oxford University Press > > A thin book (92 pages) but provides a nice overview of the field. > Probably most suited for undergraduates. > > 2. "Molecular Modeling: Principles and Applications", AR Leach, 1996, > Essex, Addison Wesley Longman Limited > > A much more robust book (595 pp) that goes into more detail than Grant and > Richards. Gives more examples and a more solid theoretical foundation for > the techniques. My choice for a graduate level textbook. > > 3. "Dynamics of Proteins and Nucleic Acids," JA McCammon and SC Harvey, > 1987, Cambridge, Cambridge University Press. > > Always a classic - an excellent (though a little dated) description of > simulations of proteins and nucleic acids. Good low level introductions to > theory with some nice examples and applications. > > 4. "Computer Simulation of Liquids", MP Allen and DJ Tildesley, 1987, > Oxford, Clarendon Press. > > Only for the hardcore simulation junkies. An excellent description of the > nuts and bolts of simulation code. Would be excellent for a course where > the students will write programs for simulations. > > 5. "Forcefield-Based Simulations," April 1997, San Diego, Molecular > Simulations Inc. > > 6. "Discover 2.9.8/96.0/4.0.0. Forcefield Simulations: User Guide, Part > 1", September 1996, San Diego, Molecular Simulations Inc. > > In my experience with teaching molecular modeling at the University of > Cincinnati, I found these user guides from MSI to be very helpful. They > give a clear explanation of forcefield based simulations. Please take a look at "Reviews in Computational Chemistry." This book series contains pedagogically driven tutorials and reviews in the area of computational chemistry. Each chapter assumes little or no previous knowledge of the topic being described and each tutorial contains a limited amount of mathematics. The series is directed toward the novice computational chemist wanting to learn about computational techniques as well as toward the seasoned professional with expertise in one topic who wants to learn about another topic. We have had chapters on important facets of computational chemistry, molecular modeling, protein modeling/engineering and drug design. More detail about what is in each volume can be found on our Web site, http://chem.iupui.edu/rcc/rcc.html F. Jensen "Introduction to Computational Chemistry" The first is probably closer to your needs. You can visit the following web-site for the second: http://bogense.chem.ou.dk/~icc Here is a link to info on molecular modeling resources http://www.chm.colostate.edu/mmac/index.html 1. Clark, Tim A handbook of Computational Chemistry, Wiley (1985). 2. Richards and Cooper, Ab Initio Molecular Orbital Calculations for Chemists, Oxford (1985) 3. Fleming, Ian Frontier Orbitals and Organic Chemical Reactions, Wiley (1976) 4. Jean, Volatron, and Burdett An Introduction to Molecular Orbitals, Oxford (19934). From chemistry-request@www.ccl.net Thu Nov 19 15:24:18 1998 Received: from njmsa.UMDNJ.EDU (root@njmsa.UMDNJ.EDU [130.219.34.100]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA09944 Thu, 19 Nov 1998 15:24:16 -0500 (EST) Received: from localhost (pyadav@localhost [127.0.0.1]) by njmsa.UMDNJ.EDU (8.8.6 (PHNE_14041)/8.8.6) with SMTP id PAA03362 for ; Thu, 19 Nov 1998 15:24:16 -0500 (EST) Date: Thu, 19 Nov 1998 15:24:16 -0500 (EST) From: Prem Yadav To: chemistry@www.ccl.net Subject: books on Mol.mod. & comp.chem. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, Following is the summary of my query about books in the area of molecular modeling, protein modeling, drug design and computational chemistry. I thank you all who responded to me. This really helped me in making my decission. Prem Yadav Molecular Mechanics Across Chemistry, by Rappe and Casewit (University Science Books, Sausalito, CA, 1997) Molecular Modelling: Principles and Applications, by Leach (Addison Wesley Longman, Essex UK, 1996). 1). Guidebook on Molecular modeling in Drug Design, edited by N. Claude Cohen, Academic Press 2). Computer Aided molecular design, Theory and applications, J. P. Doucet and J. weber, Academic Press 3). Exploring QSAR, Corwin Hansch and Albert Leo Computer-aided Molecular Design, Understanding Molecular Simulation, Molecular Modeling and Drug Design. Bioinformatics: the molecular modeling approach. > I have found the following to be most useful: > > 1. "Computational Chemistry", 1995, GH Grant and WG Richards, Oxford, > Oxford University Press > > A thin book (92 pages) but provides a nice overview of the field. > Probably most suited for undergraduates. > > 2. "Molecular Modeling: Principles and Applications", AR Leach, 1996, > Essex, Addison Wesley Longman Limited > > A much more robust book (595 pp) that goes into more detail than Grant and > Richards. Gives more examples and a more solid theoretical foundation for > the techniques. My choice for a graduate level textbook. > > 3. "Dynamics of Proteins and Nucleic Acids," JA McCammon and SC Harvey, > 1987, Cambridge, Cambridge University Press. > > Always a classic - an excellent (though a little dated) description of > simulations of proteins and nucleic acids. Good low level introductions to > theory with some nice examples and applications. > > 4. "Computer Simulation of Liquids", MP Allen and DJ Tildesley, 1987, > Oxford, Clarendon Press. > > Only for the hardcore simulation junkies. An excellent description of the > nuts and bolts of simulation code. Would be excellent for a course where > the students will write programs for simulations. > > 5. "Forcefield-Based Simulations," April 1997, San Diego, Molecular > Simulations Inc. > > 6. "Discover 2.9.8/96.0/4.0.0. Forcefield Simulations: User Guide, Part > 1", September 1996, San Diego, Molecular Simulations Inc. > > In my experience with teaching molecular modeling at the University of > Cincinnati, I found these user guides from MSI to be very helpful. They > give a clear explanation of forcefield based simulations. Please take a look at "Reviews in Computational Chemistry." This book series contains pedagogically driven tutorials and reviews in the area of computational chemistry. Each chapter assumes little or no previous knowledge of the topic being described and each tutorial contains a limited amount of mathematics. The series is directed toward the novice computational chemist wanting to learn about computational techniques as well as toward the seasoned professional with expertise in one topic who wants to learn about another topic. We have had chapters on important facets of computational chemistry, molecular modeling, protein modeling/engineering and drug design. More detail about what is in each volume can be found on our Web site, http://chem.iupui.edu/rcc/rcc.html F. Jensen "Introduction to Computational Chemistry" The first is probably closer to your needs. You can visit the following web-site for the second: http://bogense.chem.ou.dk/~icc Here is a link to info on molecular modeling resources http://www.chm.colostate.edu/mmac/index.html 1. Clark, Tim A handbook of Computational Chemistry, Wiley (1985). 2. Richards and Cooper, Ab Initio Molecular Orbital Calculations for Chemists, Oxford (1985) 3. Fleming, Ian Frontier Orbitals and Organic Chemical Reactions, Wiley (1976) 4. Jean, Volatron, and Burdett An Introduction to Molecular Orbitals, Oxford (19934).