From owner-chemistry@ccl.net Sat Aug 13 02:23:56 2005 From: "CCL" To: CCL Subject: CCL: W:Expt density of aqueous solutions Message-Id: <-28964-050813022202-16737-jTKKlThOvCLwkE03HCXsVw.:.server.ccl.net> X-Original-From: "Bhabani Mallik" Sent to CCL by: "Bhabani Mallik" Dear All, I want to know the expt density of acetone-water and methanol-water mixture with wide range of temp(from room temp to higher).If someone can give some references or sources then that help will be highly appreciated. with regards Bhabani From owner-chemistry@ccl.net Sat Aug 13 02:38:29 2005 From: "CCL" To: CCL Subject: CCL: basis set optimization using gauopt Message-Id: <-28965-050812193408-22425-jTKKlThOvCLwkE03HCXsVw\a/server.ccl.net> X-Original-From: "Dmitriy Afanasiev" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1251 Mime-Version: 1.0 Sent to CCL by: "Dmitriy Afanasiev" Dear netters, could anybody tell me how to use, at least properly execute, gauopt utility from GAUSSIAN03 utility set, please. I need to optimize exponents of some outer basis functions for particular molecule, but all my attempts to use gauopt utility for this task were unsuccessful. I also tried to follow GAUSSIAN manual step-by-step, even tried to execute example input file for gauopt utility (properly formatted, of course) but gauopt does not want to work. I used both GAUSSIAN03 for Windows and for Linux and result is the same. This is input syntax I typed: gauopt.exe output.out, according to previous posts and manual. I'm sure that my input was OK, and some problem is with syntax or gauopt utility itself. This is input file from manual: 3 3 T 0.0 0.0 7.66V 2.25V 1.24V # RHF/Gen Test Water RHF/STO-2G basis with optimized scale factors 0,1 O H,1,r H,1,r,2,a r 0.96 a 104.5 1 0 sto 1s 2 <1 12.10> sto 2sp 2 <2 12.10> **** 2 0 sto 1s 2 <3 12.10> **** 3 0 sto 1s 2 <3 12.10> **** Thank you! Dmitriy, dafanasiev\a/ukr.net From owner-chemistry@ccl.net Sat Aug 13 08:55:54 2005 From: "CCL" server.ccl.net> To: CCL Subject: CCL: Turbomole - point charges Message-Id: <-28966-050813080201-4115-jTKKlThOvCLwkE03HCXsVw<*>server.ccl.net> X-Original-From: Jana Precechtelova ncbr.chemi.muni.cz> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed MIME-Version: 1.0 Sent to CCL by: Jana Precechtelova ncbr.chemi.muni.cz> Dear CCLers, according to the Turbomole manual, one can use the $point_charges keyword in the control file to specify the location and the value of the point charges. An example from the manual is: $point_charges 0.2 0.2 0.4 2 establishes a point charge of +2 at the point 0.2 0.2 0.4 However, if I run a single point calculation using exactly this example, I see something puzzeling in the output file. Instead of the point charge 0.2 0.2 0.4 2, the output gives: ------------------------------------------------------------------------ point charges ------------------------------------------------------------------------ number of point charges read in = 1 distance threshold set to 0.10D-05 x y z charge 1.319726 0.200000 0.200000 0.000000 Self energy of the point charges: 0.00000000000 In other words, the coordinates for the location of the point charge are diffrent from what I specified in the control file. Moreover, for some reason, that I do not understand, the point charge is zero. If I try my own example with more point charges, instead of a list in the control file: $point_charges -8.342 5.400 3.375 -0.834 -8.218 4.456 3.270 0.417 -9.120 5.598 2.852 0.417 -12.030 5.482 -1.620 -0.834 -11.411 5.360 -2.340 0.417 -11.788 6.325 -1.237 0.417 . . . . . -13.923 10.859 -1.284 -0.834 -13.568 11.307 -0.516 0.417 -13.169 10.417 -1.673 0.417 -11.571 11.052 0.707 -0.834 -10.903 11.147 1.386 0.417 -11.368 11.740 0.074 0.417 I get the following list in the output: ------------------------------------------------------------------------ point charges ------------------------------------------------------------------------ number of point charges read in = 45 distance threshold set to 0.10D-05 x y z charge 0.000000 -8.342000 5.400000 0.000000 3.375000 -8.218000 4.456000 -0.834000 3.270000 -9.120000 5.598000 0.417000 2.852000 -12.030000 5.482000 0.417000 -1.620000 -11.411000 5.360000 -0.834000 -2.340000 -11.788000 6.325000 0.417000 . . . . . -1.660000 -13.923000 10.859000 0.417000 -1.284000 -13.568000 11.307000 -0.834000 -0.516000 -13.169000 10.417000 0.417000 -1.673000 -11.571000 11.052000 0.417000 0.707000 -10.903000 11.147000 -0.834000 1.386000 -11.368000 11.740000 0.417000 Self energy of the point charges: -9.28113946401 Does someone what's hapenning - why the output information differ from my input? BTW, I specified the point charges in the control file manually, does someone know, how to generate them using define? Thanks for any hint, Jana ============================================================= Jana Precechtelova (Ph.D. student) ------------------------------------------------------------- Institut fuer Anorganische Chemie Bayerische Julius-Maximilians Universitaet Wuerzburg Am Hubland, 97074 Wuerzburg, Germany & NMR Laboratory National Centre for Biomolecular Research (NCBR) Faculty of Science, Masaryk University Kotlarska 2, 611 37 Brno, Czech Republic ============================================================= email: janap<*>ncbr.chemi.muni.cz ============================================================= From owner-chemistry@ccl.net Sat Aug 13 11:22:11 2005 From: "CCL" To: CCL Subject: CCL: ArgusLab publc API ? Message-Id: <-28967-050813111421-30987-jTKKlThOvCLwkE03HCXsVw_-_server.ccl.net> X-Original-From: Mark Thompson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed MIME-Version: 1.0 Sent to CCL by: Mark Thompson I'm gauging the interesting in a new way to distribute ArgusLab. ArgusLab is composed of components that interact via APIs. For example there is a component that can calculate UV/vis spectra, a component that does AM1, PM3, etc., a component that does the molecular docking, a component that handles all atom typing, molecular topology, protonation states. Is there any interest from the general user community for my distributing these components with public APIs so that they can be integrated into other applications and web services? What would be required to get them to run under MOE for example? The code is generally Windows-free (all the Windows-specific code is in the ArgusLab windowing interface). The components could be distributed as Windows DLL, COM DLL, Unix shared libs, and even with a web services API. Please let me know what you think? Cheers, Mark ---------------------------- Mark Thompson mark_-_arguslab.com http://www.arguslab.com ----------------------------