From owner-chemistry@ccl.net Wed May 30 03:56:01 2007 From: "Weill Nathanael naweill:+:gmail.com" To: CCL Subject: CCL: Binding site Message-Id: <-34369-070529130537-7302-MIm+GacTAQtbcqK5SQJpfQ]^[server.ccl.net> X-Original-From: Weill Nathanael Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 29 May 2007 18:10:22 +0200 MIME-Version: 1.0 Sent to CCL by: Weill Nathanael [naweill**gmail.com] Hy, I asked a friend more specialist, he answers me : -Surfnet (you have to register first) -Voidoo -Pocket -CASTp (web site) I did not test it... Best regards Nathanael Weill Zuccotto, Fabio Nervianoms Fabio.Zuccotto]*[nervianoms.com a écrit : > Hello CCL - I was wondering if there is a good quality software > (possibly free) that allows to: > - identify cavities on a protein surface > - calculate the volume of the cavities > > Thank you > > Fabio From owner-chemistry@ccl.net Wed May 30 07:15:01 2007 From: "Wai-To Chan chan_+_curl.gkcl.yorku.ca" To: CCL Subject: CCL: A Comprehensive book on theoretical chemistry Message-Id: <-34370-070530071056-23689-v72+HBuunBBanEtnstxQkQ _ server.ccl.net> X-Original-From: Wai-To Chan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Wed, 30 May 2007 07:53:10 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Wai-To Chan [chan**curl.gkcl.yorku.ca] <<<<<<<<<<<<<<<<<<<<<<<<<<<<< Hi, I am a senior pharmacy undergrad, Minia, Egypt. I am studting theoretical chemistry independently as I hope I pursue my PhD research in it. I am currently studying books like Introduction to Computational Chemistry, Frank Jensen, Essentials of Computational Chemistry, Christopher Cramer, and some web material. I am really looking for a book that provides a comprehensive view on computational techniques and methods, including essentials of theory and formalism, in addition to exercises and worked examples, meaningly, a book that helps me teach myself the subjet. Noteworthy, I have already get a good knowledge base in math, Computer Science and quantum mechanics, in addition to the fundamentals of the electronic structure theory. thanks in advance >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For some years one might expect a BSc holder graduating from a 'standard' chemistry program in a decent North American university to possess a familarity of the basics in theoretical chemistry at the level of the quantum chemistry textbook by Levine and the statistical thermodynamics text by McQuarrie. In my own schooling other courses outside chemistry which I consider important to post-graduate research include Fortran programming, differential equations and vector calculus. To this day I still kick myself for not taking any 2nd year physics courses in E&M and special relativity. In reality standard varies. Nowadays advanced physical chemistry courses in statistical mechanics and quantum chemistry are seldom required in a typical chemistry curriculum Here in Canada I've seen people who had no difficulties completing a phd in the field of computational quantum chemistry without any formal schooling in quantum chemistry beyond McQuarrie's introductory text and without writing a single line of code. So if you have a good basic knowledge of quantum chemistry at a level comparable to Levine, Pilar or John Lowe you are already reasonably well equipped for graduate studies by the standard here. My impression is that theoretical chemistry research has attained a level of maturity in the field of the application of quantum chemistry such that a rigorous study of the fundamentals is not always absolutely essential although some exposure is certainly desirable. I would suggest you to tailor your study to the area of interest you intend to pursue. Suppose you are looking to graduate research in methodological developments in electronic structure theory and you want to engage in the coding of a sophisticated ccsd(t) method in a quantum chemistry package. In such case a mastery of the theries beyond elementary quantum chemistry text in a book like "Methods of molecular quantum mechanics" by Roy McWeeny (which includes extensive problem sets) should be very helpful. If on the other hand you are interested in something less theoretical say a project that involves applying theory to biochemistry you might be more concerned with the aspects of the execution of various quantum chemistry softwares. The level of understanding of the background theory required really depends on the nature of your research. In computational quantum chemistry research it is usually an understanding of Pople's model chemistry rather than the underlying mathematics of the model employed that enables a laboratory chemist to obtain and interpret the computational results. Chance is you have more to worry about understanding the chemistry than the theory you are applying. Your choice of Jensen and Cramer for your self-study seems fine. It may be prudent if you can supplement your study through running computations with a quantum chemistry program such as GAMESS. Experience in the implementation of free quantum chemistry software in Linux should help you to prepare for future research. You could for instance install GAMESS on a PC and use the program to try out some problems described in a quantum chemistry text. You can also learn to install other useful (and free) softwares such as MOLDEN for the visualization of output files from running GAMESS. There are other areas in theoretical chemistry which place less emphasis on quantum chemistry. I don't think there is any single comprehensive theoretical chemistry that will give you an overview of the entire field. However you may take a look on "Quantum Mechanics in Chemistry" by George Schatz and Mark Ratner. This textbook is unique in that it cover concepts other than those of quantum chemistry and should provide a good starting point if you want to pursue research in areas that deal with chemical dynamics. Wai-To Chan From owner-chemistry@ccl.net Wed May 30 10:52:00 2007 From: "Jeff Hammond jeff.science ~ gmail.com" To: CCL Subject: CCL: A Comprehensive book on theoretical chemistry Message-Id: <-34371-070530103701-28651-vM3/tXIrCgSWsd3ROYoPGA|-|server.ccl.net> X-Original-From: Jeff Hammond Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Wed, 30 May 2007 09:36:23 -0500 MIME-Version: 1.0 Sent to CCL by: Jeff Hammond [jeff.science**gmail.com] Mustafa, I agree with Alexandr that the purple book (Helgaker/Jorgensen/Olsen) is the best resource available short of an extensive collection of the Journal of Chemical Physics. However, big purple costs about $400. I found that the ESQC Lecture Notes (http://www.teokem.lu.se/esqc/book/) are an excellent substitute for less money. You'll find some of the same content for reasons that will be quite obvious upon inspection. Szabo and Ostlund is a classic and is the best thing you can get for $11. It doesn't cover either of the moderns standards, DFT and coupled-cluster, but it does cover SCF, CI and MPn in a very straightforward way. I recommend these online lecture notes: copy 1: http://zopyros.ccqc.uga.edu/lec_top/lectures.html copy 2: http://www.ccc.uga.edu/lec_top/ alternate version: http://vergil.chemistry.gatech.edu/notes/ The last link also has good references on coding. It's slightly old, but "Modern Electronic Structure Theory I & II" by David Yarkony are also good books, particularly if you're interested in MCSCF or MRCI methods. These are the best two books for DFT and the former gives a good introduction to the basics of electronic structure: "Density-Functional Theory of Atoms and Molecules" by Robert Parr and Weitao Yang "A Chemist's Guide to Density Functional Theory" by Wolfram Koch and Max Holthausen I recommend the following articles if you want to be current on one of the standard models in the field: "Coupled-Cluster Approach to Molecular Structure and Spectra: A Step toward Predictive Quantum Chemistry," R. J. Bartlett, J. Phys. Chem. 93, 1697 (1989). "Coupled-cluster theory in quantum chemisty," Bartlett and Musial, Reviews of Modern Physics 79, 291 (2007). If you don't have access to these articles, let me know and I will email you the PDFs. If you're a fan of history, this is a very interesting read and puts a lot of things in perspective: QUANTUM CHEMISTRY: Classic Scientific Papers translated and edited by Hinne Hettema http://www.worldscibooks.com/chemistry/3201.html I also like this website: http://www.quantum-chemistry-history.com/ Finally, whenever it appears, this should be a very good book: I. Shavitt and R.J. Bartlett, “Many-Body Methods in Quantum Chemistry,” Cambridge Press, June 2006. I apologize for using potentially unfamiliar acronyms, but Google and Wikipedia should be able to elucidate them immediately. Jeff > Sent to CCL by: "Mustafa Hussein" [mustafa.hussein86---yahoo.com] > Hi, > I am a senior pharmacy undergrad, Minia, Egypt. I am studting theoretical chemistry independently as I hope I pursue my PhD research in it. > I am currently studying books like Introduction to Computational Chemistry, Frank Jensen, Essentials of Computational Chemistry, Christopher Cramer, and some web material. > I am really looking for a book that provides a comprehensive view on computational techniques and methods, including essentials of theory and formalism, in addition to exercises and worked examples, meaningly, a book that helps me teach myself the subjet. Noteworthy, I have already get a good knowledge base in math, Computer Science and quantum mechanics, in addition to the fundamentals of the electronic structure theory. > > thanks in advance > > Mustafa Hussein > mustafa.hussein86===yahoo.com > Faculty of Pharmacy, > Minia University > Minia 61511, Egypt From owner-chemistry@ccl.net Wed May 30 12:26:01 2007 From: "Liisa laakkonen llaakkon::cc.helsinki.fi" To: CCL Subject: CCL: show ruler in VMD Message-Id: <-34372-070530031012-8511-YXbJnbOmsC5hbBy4FCLfLA:_:server.ccl.net> X-Original-From: Liisa laakkonen Content-Type: text/plain; charset=us-ascii Date: Wed, 30 May 2007 09:33:09 +0300 Mime-Version: 1.0 Sent to CCL by: Liisa laakkonen [llaakkon===cc.helsinki.fi] Hello Yubo, I've done the angstrom ruler simply by building a dummy pdb with enough points to measure the desired distance, and displaying it side by side with my molecule. Works equally well for a compass. Greetings, Liisa liisa.laakkonen__helsinki.fi On Tue, May 29, 2007 at 09:29:44AM -0400, Chelsey Crosse cmcrosse*_*mtu.edu wrote: > Yubo, > > The only way that I know of to put a ruler in VMD by opening the Tcl > console and drawing it in yourself. However, I'm not positive about > how accurate you can make it. > > Chelsey > > On 25 May 2007, at 10:17, Yubo Fan yubofan(0)mail.chem.tamu.edu wrote: > > > Hello, > > > > A quick question about VMD. Is there any way to show ruler (ie > > angstroms in unit) in VMD window? > > > > Thanks, > > > > Yubo > > ============================================================ > > Dr. Yubo Fan Email: yubofan^^^mail.chem.tamu.edu > > Department of Chemistry Tel: 1-979-845-5237 > > Texas A&M University > > College Station, TX 77843 > > ============================================================ > > > From owner-chemistry@ccl.net Wed May 30 13:01:00 2007 From: "Alban Arrault alban.arrault]*[univ-orleans.fr" To: CCL Subject: CCL: Binding site Message-Id: <-34373-070529121121-29994-bGPL7hcygXq72fXhx+mVww^_^server.ccl.net> X-Original-From: Alban Arrault Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 29 May 2007 17:42:48 +0200 MIME-Version: 1.0 Sent to CCL by: Alban Arrault [alban.arrault/./univ-orleans.fr] Hello Fabio, you can identify cavities online with CASTp (Computed Atlas of Surface Topography of proteins) for free and I am not sure but Arguslab should calculate the solvent accessible surfaces. Alban Zuccotto, Fabio Nervianoms Fabio.Zuccotto]*[nervianoms.com a écrit : > Hello CCL - I was wondering if there is a good quality software > (possibly free) that allows to: > - identify cavities on a protein surface > - calculate the volume of the cavities > > Thank you > > Fabio From owner-chemistry@ccl.net Wed May 30 13:36:00 2007 From: "Demetrios Xenides Demetrios.Xenides%%uop.gr" To: CCL Subject: CCL: ReA Comprehensive book on theoretical chemistry Message-Id: <-34374-070530071631-24756-bZMeoVZlwuoNRB7XLCznmw:+:server.ccl.net> X-Original-From: Demetrios Xenides Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Wed, 30 May 2007 13:13:23 +0300 MIME-Version: 1.0 Sent to CCL by: Demetrios Xenides [Demetrios.Xenides]|[uop.gr] May be this one might be a good choice.... Rode, B.M. / Hofer, T. / Kugler, M.: The Basics of Theoretical and Computational Chemistry ISBN: 978-3-527-31773-8 2007. Hardcover. UP € 59.00 / sFr 94.00 Discounted price € 50.20 From owner-chemistry@ccl.net Wed May 30 14:10:00 2007 From: "Victor Medel Juarez vmedel[a]cinvestav.mx" To: CCL Subject: CCL:G: keyword print exchange-correlation ehnergy Message-Id: <-34375-070530132258-25672-Qb7itTntkoTOUqQkH/hMxg\a/server.ccl.net> X-Original-From: "Victor Medel Juarez" Date: Wed, 30 May 2007 13:22:54 -0400 Sent to CCL by: "Victor Medel Juarez" [vmedel(-)cinvestav.mx] Hola, I would like to know how to print the exchange-correlation ehnergy in gaussian. Thanks From owner-chemistry@ccl.net Wed May 30 18:28:00 2007 From: "Mustafa Hussein mustafa.hussein86-$-yahoo.com" To: CCL Subject: CCL: Running GAMESS on Windows Message-Id: <-34376-070530182503-16241-lyMXarAeT178SMbS3XKKkg*server.ccl.net> X-Original-From: "Mustafa Hussein" Date: Wed, 30 May 2007 18:25:00 -0400 Sent to CCL by: "Mustafa Hussein" [mustafa.hussein86,yahoo.com] Hi, I have got a copy of GAMESS. I need to run it on Windows; is it possible? If it is, I appreciate if you tell me how. Thanks Mustafa From owner-chemistry@ccl.net Wed May 30 20:33:00 2007 From: "Alexandr Isayev alex(_)ccmsi.us" To: CCL Subject: CCL: Running GAMESS on Windows Message-Id: <-34377-070530202928-11686-1R4IqcLSQ7t8nU1vHTpwLA _ server.ccl.net> X-Original-From: Alexandr Isayev Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Wed, 30 May 2007 19:27:58 -0500 MIME-Version: 1.0 Sent to CCL by: Alexandr Isayev [alex*_*ccmsi.us] Mustafa, Get a PC GAMESS from Alexandr Granovsky http://classic.chem.msu.su/gran/gamess/ It natively runs under windows environment and has comprehensive manual. However for future production work, make sure to learn what is *nix, and you can eat it :^) hope this will help, Alexandr Wednesday, May 30, 2007, 5:25:00 PM, you wrote: MHmhyc> Sent to CCL by: "Mustafa Hussein" [mustafa.hussein86,yahoo.com] MHmhyc> Hi, MHmhyc> I have got a copy of GAMESS. I need to run it on Windows; is MHmhyc> it possible? If it is, I appreciate if you tell me how. MHmhyc> Thanks MHmhyc> Mustafa MHmhycMHmhycMHmhycMHmhycMHmhycMHmhycMHmhycMHmhycMHmhycMHmhycMHmhycMHmhycMHmhyc> Conferences: MHmhyc> http://server.ccl.net/chemistry/announcements/conferences/ MHmhycMHmhycMHmhycMHmhycMHmhyc------------------------------------------------------- Alexandr Isayev, Graduate Research Assistant, and System Administrator ,+, Computational Center for Molecular Structure and Interactions (CCMSI), Jackson State University, Jackson, MS USA Tel: +(601) 979-1134 e-mail: alex(at)ccmsi.us Web: http://www.ccmsi.us -------------------------------------------------------- From owner-chemistry@ccl.net Wed May 30 21:16:00 2007 From: "Mustafa Hussein mustafa.hussein86- -yahoo.com" To: CCL Subject: CCL: GAMESS on Intel Celeron Processors Message-Id: <-34378-070530211302-31073-HOv3Yg/jXLa7hfxjH5TCJQ~~server.ccl.net> X-Original-From: "Mustafa Hussein" Date: Wed, 30 May 2007 21:12:59 -0400 Sent to CCL by: "Mustafa Hussein" [mustafa.hussein86-.-yahoo.com] Hi, I have checked some specifications on installing GAMESS. I wonder if it can be run on Intel Celeron processors or not. I need some help Thanks Mustafa