From owner-chemistry@ccl.net Thu Jan 4 12:26:00 2007 From: "Kurt De Grave kurt.degrave_-_pharmadm.com" To: CCL Subject: CCL: compound library cherry picking Message-Id: <-33326-070103153620-28841-KFVCTcC3yMw1iONrmBIlNw]|[server.ccl.net> X-Original-From: "Kurt De Grave" Date: Thu, 4 Jan 2007 10:38:40 -0500 Sent to CCL by: "Kurt De Grave" [kurt.degrave-x-pharmadm.com] Hi, DMax Chemistry Assistant (TM) now supports compound library cherry picking. It is now possible to prioritize a vast library based on a self-built model or expert system. As before, the model can contain arbitrarily complex substructures and properties, not just fingerprints. URL: http://www.pharmadm.com/DMaxChemistryAssistant.asp The tutorial is available online: http://www.pharmadm.com/products/DMax/ChemistryAssistant/tutorial/tutorial_index.html kurt. From owner-chemistry@ccl.net Thu Jan 4 13:00:01 2007 From: "Caldwell, Richard A caldwell||utdallas.edu" To: CCL Subject: CCL: "Experiments" in Quantum Chemistry for Non-chemists? Message-Id: <-33327-070103153620-28842-2JX7+F8Y15TXmMuPf+bhSg.@.server.ccl.net> X-Original-From: "Caldwell, Richard A" Date: Thu, 4 Jan 2007 10:05:56 -0600 MIME-Version: 1.0 Sent to CCL by: "Caldwell, Richard A" [caldwell[a]utdallas.edu] [CCL admin removed the useless winmail.dat attachment] If you look into the Spartan tutorials you might find some experiments that are adaptable to your purposes. http://www.wavefun.com/ Dick Caldwell -----Original Message----- From: Christoph Weber weber+*+scripps.edu [mailto:owner-chemistry(!)ccl.net] Sent: Wed 1/3/2007 2:37 PM To: Caldwell, Richard A Subject: CCL: "Experiments" in Quantum Chemistry for Non-chemists? Sent to CCL by: Christoph Weber [weber{=}scripps.edu] Why not keep it simple and leave out the "experiment" and possibly "quantum chemistry" aspects? Concentrate instead on visualizing and exploring molecular structure and function and build on people's existing knowledge of certain molecules and how to navigate in 3D on a computer. Kids especially have a very good sense of 3D on the screen due to their gaming experience, and you can leverage this easily. I've successfully presented interactive molecular graphics workshops to kids as young as 12. My 2 cts. Christoph > -----Original Message----- >> From: owner-chemistry|ccl.net [mailto:owner-chemistry|ccl.net] > Sent: 21 d=E9cembre, 2006 09:55 > To: Axel Mathieu > Subject: CCL: "Experiments" in Quantum Chemistry for Non-chemists? > > Sent to CCL by: Ralf Tonner [Tonner-x-chemie.uni-marburg.de] > Dear CCLers, > > since a few years the "Chemikum" exists at the University of > Marburg (www.chemikum-marburg.de) as a possibility for > pupils, adults and kids to learn to know the experimental > world of chemistry and do some instructive experiments on > their own. > > As a further extension to this project, our group has been > asked to contribute with an "experiment" or interesting > presentation from the computational chemistry side. > > As all of you know, presenting our topics even to chemists > can be a tedious task, so I was searching the web for nice > didactic "experiments" on the computer but unsuccessful up > to know. > > Is anyone aware of a resource where to fetch some ideas or > publicly available presentations/experiments which fulfill > the requirements of being finished in at most half an hour > without any pre-knowledge in quantum chemistry and at best > let non-chemists gain some insight ? > > I would hardly have the time and educational knowledge of > setting up something completely from scratch... > so I am very grateful for any suggestions. > > Thanks for your help > > Ralf. -- | Dr. Christoph Weber Sen. Applications Specialist | Research Computing, TPC21 858-784-9869 (phone) | The Scripps Research Institute 858-784-9301 (FAX) | La Jolla CA 92037-1027 weber\a/scripps.edu | http://www.scripps.edu/~weber/ The only reason for time is so that everything doesn't happen at once. - Albert Einstein From owner-chemistry@ccl.net Thu Jan 4 13:48:00 2007 From: "Andrew D. Fant fant%%pobox.com" To: CCL Subject: CCL: Cleanup of Threaded Protein Models Message-Id: <-33328-070104133135-5951-1oayn+DcuXTPNn4vRaCnRg:+:server.ccl.net> X-Original-From: "Andrew D. Fant" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 04 Jan 2007 13:00:33 -0500 MIME-Version: 1.0 Sent to CCL by: "Andrew D. Fant" [fant**pobox.com] Afternoon all, I'm looking at a set of protein structural models produced by a collection of threading methods. As I understand it, the received advice from the community is that attempting to refine the models via MD simulation tends to push the model further away from the actual structure. Does this advice hold for simple forcefield minimizations as well? Before I start doing anything fancy, I'd like to be sure that I have something sane to work from. I know that prochek can flag potential problems, but I'd rather not be tied to one tool for this. Thanks in advance, Andy -- Andrew Fant | And when the night is cloudy | This space to let Molecular Geek | There is still a light |---------------------- fant%x%pobox.com | That shines on me | Disclaimer: I don't Boston, MA | Shine until tomorrow, Let it be | even speak for myself From owner-chemistry@ccl.net Thu Jan 4 16:32:01 2007 From: "errol lewars elewars:trentu.ca" To: CCL Subject: CCL:G: G03:freq calculations Message-Id: <-33329-070103104818-30644-egZt7QSKu18nkgup2XZMNw:_:server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 03 Jan 2007 10:13:23 -0500 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars/a\trentu.ca] 2006 Jan 3 You did not say what your molecule is or what your program is (it looks like Gaussian). If applicable, you could try running the molecule within its symmetry (rather than ignoring symmetry). You could also try using more (or less!) memory and see what happens. Very long times for frequencies are "reasonable". E. Lewars ===== soumya s soumya_samineni_._rediffmail.com wrote: >Sent to CCL by: "soumya s" [soumya_samineni-x-rediffmail.com] >Dear people, >Naive question ... sry. >I try to run a freq calculation on porphyrin > >%nproc=8 >%mem=8MW >opt freq b3lyp/6-31g* nosymm > >0 1 >....... >........ > >and the frequency calculation took almost 10hrs (is this resonable!!).. how can i make the calculations run better (other than increasing the no. of procs..) > >thanx in advance> > > > > From owner-chemistry@ccl.net Thu Jan 4 19:19:00 2007 From: "Sean M Rathlef sean|-|syncitium.net" To: CCL Subject: CCL: enzyme kinetics in silico Message-Id: <-33330-070104183151-13835-xapZ3yDRNfbhWXKW6Xwaog]_[server.ccl.net> X-Original-From: "Sean M Rathlef" Date: Thu, 4 Jan 2007 18:31:47 -0500 Sent to CCL by: "Sean M Rathlef" [sean+*+syncitium.net] Greetings: Our group is nearing completion of a beta platform which will enable users to model enzyme kinetics constants (Km, Vmax, Ki, etc) on a computer as opposed to in the laboratory. It is the first such process of its kind. The simulations conduit is based on peer reviewed computational chemistry, and the enzyme kinetic scaffolds are based on the expert input of Dr. Wallace Cleland -- the worlds most comprehensively published enzyme kinetic theorist. At present, we are seeking to identify prospective users for this technology. The methods will be included in an intuitive interface, whereby users will be able to model their enzymes and generate their kinetic data using a predefined set of software methods. Again, this is the first such platform of its kind, and we are hoping that the beta will be available for evaluation in a few weeks time. If any of you are interested in hearing more, or would like to be included on our list of future evaluators, please send me an email with your contact information to sean++syncitium.net. Thanks in advance, and we look forward to hearing from you soon. Sean --------------------------------------------------- Sean Rathlef MSc Managing Director Syncitium, Inc. --------------------------------------------------- Tel: 250.516.2466 Email: sean++syncitium.net URL: http://www.syncitium.net ---------------------------------------------------