From owner-chemistry@ccl.net Tue Apr 8 02:49:00 2008 From: "Madhurima Jana rima!=!chem.iitkgp.ernet.in" To: CCL Subject: CCL:G: Calculation of force constants using Gaussian03 Message-Id: <-36665-080408021350-31982-xMFnDSYB5PWkSHn8UzDnNw(~)server.ccl.net> X-Original-From: Madhurima Jana Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Tue, 8 Apr 2008 10:59:11 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Madhurima Jana [rima*|*chem.iitkgp.ernet.in] Hi Are there any methods or modules regarding the calculation of force constants for bond length, bond angle, torsion and Lennard-Jonnes parameters in Gaussian03? Thanks in advance, Madhurima -- =========================================================================== | Madhurima Jana | | | Department of Chemistry | | IIT Kharagpur | | Kharagpur:721302 | | Email: rima===chem.iitkgp.ernet.in | =========================================================================== From owner-chemistry@ccl.net Tue Apr 8 03:24:00 2008 From: "Lukasz Cwiklik cwiklik a gmail.com" To: CCL Subject: CCL:G: projected vs. unprojected MPn benchmarks? Message-Id: <-36666-080408030035-7447-4X4PxMtV4LHfK0NH/45eaA*server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 8 Apr 2008 10:00:03 +0300 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [cwiklik ~~ gmail.com] > Sent to CCL by: Mariusz Radon [mariusz.radon^gmail.com] > Dear CCL-ers: > > I'm looking for benchmark studies on projected vs. unprojected MP2-MP4 > for the UHF reference function. (By projected I mean the energies > called ``PMPn'' in Gaussian output, while the unprojected are called > ``UMPn''.) Dear Mariusz, Maybe it is not a benchmark study but there is a comparison of UMP2 and PMP2 (with CASPT2, MRCI and experimental data) for both adiabatic and vertical IP of imidazole in water in our last paper which is currently in press in JPhysChemA: http://pubs.acs.org/cgi-bin/abstract.cgi/jpcafh/asap/abs/jp711476g.html If you have further questions, ask Basia who was doing this part in the paper. Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com From owner-chemistry@ccl.net Tue Apr 8 04:04:00 2008 From: "Lukasz Cwiklik cwiklik*gmail.com" To: CCL Subject: CCL:G: Calculation of force constants using Gaussian03 Message-Id: <-36667-080408035440-22461-Zx1pI0RGXI/YDJEMAO4sXw^server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 8 Apr 2008 10:48:12 +0300 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [cwiklik]*[gmail.com] On Tue, Apr 8, 2008 at 8:29 AM, Madhurima Jana rima!=!chem.iitkgp.ernet.in wrote: > > Sent to CCL by: Madhurima Jana [rima*|*chem.iitkgp.ernet.in] > > Hi > > Are there any methods or modules regarding the calculation of force > constants for bond length, bond angle, torsion and Lennard-Jonnes parameters > in Gaussian03? Dear Madhurima, Usually there is neither general nor easy path leading from ab initio results to Lennard-Jones and other force field parameters. If your molecule is a "standard" organic one you can try to use GAFF/Antechamber from Amber package to construct a force field. In this procedure Gaussian is used in order to generate geometry parameters and charge distribution. Here is the link (see Tutorial & Examples there): http://amber.scripps.edu/antechamber/example.html Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com From owner-chemistry@ccl.net Tue Apr 8 09:57:00 2008 From: "Durairajan Senthilnathan zenthil03%%yahoo.co.in" To: CCL Subject: CCL: Linearised basis sets for NBO calculation Message-Id: <-36668-080408095440-17119-46SE5f8Q5QZTUXYuIMsitw-.-server.ccl.net> X-Original-From: "Durairajan Senthilnathan" Date: Tue, 8 Apr 2008 09:54:36 -0400 Sent to CCL by: "Durairajan Senthilnathan" [zenthil03-x-yahoo.co.in] Dear CCL'rs I have a error during NBO calculation of some highly delocalised transition states. I have error in my out put file as "NBO canot handle linearly depandant basis sets". I have used for this calculation b3lyp/6-31g*(2d, p) basis set. How can I aviod this error. any one you tell me a better solution regarding my problem. best wishes from Bharathidasan University From owner-chemistry@ccl.net Tue Apr 8 17:29:01 2008 From: "Kalju Kahn kalju[#]chem.ucsb.edu" To: CCL Subject: CCL: OPLS/AA Validation Data Message-Id: <-36669-080407200304-20046-hfN7HZ/8nwubscc8pMREtA _ server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 7 Apr 2008 16:26:45 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju^chem.ucsb.edu] Hi Dan, I am not aware of a central repository of validation for OPLS-AA but there are two pieces from my work that might be helpful: 1) Table 4 from "Parameterization of OPLS-AA force field for the conformational analysis of macrocyclic polyketides" in JCC 23, 977 (2002) gives exp data for liquid densities and heats of vaporization. The Table gives results with a modified force field but the original implementation was also good in this area. Let me know if you'd like me to dig up the details. The Supplementary Material of this paper has structures and energies of molecules I used. 2) Table 6 in "Improved efficiency of focal point conformational analysis with truncated correlation consistent basis sets" in JCC 29, 900 (2008) compares OPLS-AA against rather accurate QM. The OPLS-AA RMSD error from this data set (0.61 kcal/mol) was about twice the RMSD of MMFF. Best regards, Kalju > Hello CCL, > > > > I am interested in obtaining some reference data that can be used to > validate an implementation of the OPLS/AA force-field. As an example of > what I mean, a suite of data for the MMFF94 force field exists online: > > > > http://www.ccl.net/cca/data/MMFF94/ > > > > I have been unable to get such a data set for the OPLS/AA force field >> from the authors, and I have been unsuccessful finding anything useful > on the web or in any related papers that I know of. We would prefer not > to have to buy an expensive piece of software merely for the purpose of > generating this data. > > > > Does anyone know how I can obtain some data in order to validate an > implementation of the OPLS/AA force field? > > > Sincerely, > > Dan > > Daniel M. Oberlin > CambridgeSoft Corporation > 100 CambridgePark Drive > Cambridge, MA 02140 USA > 617.259.9959 > dmoÊmbridgesoft.com > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106