From owner-chemistry@ccl.net Sun Aug 1 04:05:00 2010 From: "morteza moghimi m.moghimi.w[a]gmail.com" To: CCL Subject: CCL:G: nbo5 error in linke 607 for g09&g03 Message-Id: <-42397-100801040253-19342-+O32wg+ERvvT0d86pEtzKg|*|server.ccl.net> X-Original-From: "morteza moghimi" Date: Sun, 1 Aug 2010 04:02:51 -0400 Sent to CCL by: "morteza moghimi" [m.moghimi.w---gmail.com] Hi, everyone i have a problem for nbo5 input i cant build input without error at the end of the output occure an error that is (( Error: Unrecognizable keyword >>CMO << Program must halt. Error Error termination via Lnk1e in C:\G03W\l607.exe)) i need a correct input for cmo calculation please help me thanks in advance From owner-chemistry@ccl.net Sun Aug 1 09:40:00 2010 From: "W Flak williamflak-x-yahoo.com" To: CCL Subject: CCL: Dipole moment Message-Id: <-42398-100801093856-30653-5QLesAwJ6EbfDqGYACnAqA.@.server.ccl.net> X-Original-From: "W Flak" Date: Sun, 1 Aug 2010 09:38:55 -0400 Sent to CCL by: "W Flak" [williamflak-$-yahoo.com] Dear CCL users I am comparing the dipole moment generated by RESP (AMBER) for some molecules with those generated by HF/6-31G*. During ESP calculation using: #p hf/6-31G* geom=connectivity scf=tight pop=mk iop(6/33=2,6/41=10,6/42=17) I got an output containing the following sections ************ Charge= 0.0000 electrons Dipole moment (field-independent basis, Debye): X= 0.0000 Y= 0.0000 Z= -4.2913 Tot= 4.2913 ************ Fitting point charges to eletrostatic potential Charges from ESP fit, RMS= 0.00167 RRMS= 0.12389: Charge= 0.00000 Dipole= 0.0000 0.0000 -4.4250 Tot= 4.4250 ************ Why the dipole moments are different? Which one is more accurate? As I understand, point charges are fitted to generate the electrostatic and dipole moment of the molecule, so the dipole moment shouldn't change, am I missing something? I didn't find any article on this point. Any kind of help would be appreciated. Thanks in advance W. Flak From owner-chemistry@ccl.net Sun Aug 1 13:43:00 2010 From: "Jacco van de Streek vandestreek]![avmatsim.de" To: CCL Subject: CCL:G: Dipole moment Message-Id: <-42399-100801134134-15369-+GhX4eaWQ3iMthEwCRFPIQ/a\server.ccl.net> X-Original-From: Jacco van de Streek Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 01 Aug 2010 19:41:25 +0200 MIME-Version: 1.0 Sent to CCL by: Jacco van de Streek [vandestreek###avmatsim.de] On 08/01/2010 03:38 PM, W Flak williamflak-x-yahoo.com wrote: > As I understand, point charges are fitted to generate the electrostatic and dipole moment of the molecule, so the dipole moment shouldn't change, am I > missing something? If this is Gaussian, in order to add the constraint that the atomic point charges reproduce the QM dipole moment exactly, you need to write: pop=(mk,dipole) (At least when I last used Gaussian, which is a couple of years ago). I think this also answers your two other questions. It's probably even better to choose: pop=(chelpg,dipole) Best wishes, -- Dr Jacco van de Streek Senior Scientist Avant-garde Materials Simulation Freiburg im Breisgau, Germany From owner-chemistry@ccl.net Sun Aug 1 15:59:01 2010 From: "Alberto Sergio Garay sgaray(0)fbcb.unl.edu.ar" To: CCL Subject: CCL: Request for Deuterium Order parameters of ETHER LIPIDS.. Message-Id: <-42400-100731161637-10839-uLKFsMDRELJaYPQRwkrGLA:_:server.ccl.net> X-Original-From: Alberto Sergio Garay Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Sat, 31 Jul 2010 17:16:27 -0300 MIME-Version: 1.0 Sent to CCL by: Alberto Sergio Garay [sgaray^^fbcb.unl.edu.ar] Thanks to Dr. Venable, Dr Mannock and Dr. Hood for their reading suggestion. I hope I'll be reading these books and paper very soon. -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 Mensaje escrito por: "Venable, Richard (NIH/NHLBI) E venabler(0)nhlbi.nih.gov" : > > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler#,#nhlbi.nih.gov] > > The work of Joachim and Anna Seelig starting in the 1970's is often > considered one of the most significant collections of 2H NMR > measurements on lipids. Their early work included a chemical > synthesis tour de force in placing deuterium at specific chain > positions in order to validate the signal assignments. You should > definitely include the author name of Seelig in literatures searches > for lipid order parameters. > > -- > Rick Venable 5635 FL/T906 > Membrane Biophysics Section > NIH/NHLBI Lab. of Computational Biology > Bethesda, MD 20892-9314 U.S.A. > > > On 7/30/10 8:37 PM, "Barry Hardy barry.hardy*o*vtxmail.ch" > wrote: > Sent to CCL by: David Mannock [dmannock-.-ualberta.ca] > > Sergio, Look at some of Harold Jarrell's papers in the 1980s. He did a > lot of glycolipid 2H-NMR, but will have cited PL work. You should be > able to trace the references back and forward through their citations. > David Mannock > > On 7/30/2010 6:20 AM, Alberto Sergio Garay sgaray===fbcb.unl.edu.ar wrote: >> Sent to CCL by: Alberto Sergio Garay [sgaray^^^fbcb.unl.edu.ar] >> >> I'm looking for Deuterium Order parameters of Ether lipids' tails but >> without success. I need it in order to test some of my Molecular >> Dynamics simulations of DHPC (Dihexadecyl-Phosphatidylcholine). >> >> Please, if someone know about some papers (or experimental values not >> published) where some of this parameters are shown, I would very >> appreciate this help. >> >> Sergio> > > From owner-chemistry@ccl.net Sun Aug 1 16:33:00 2010 From: "Marcin Sterniczuk m.sterniczuk:+:ichtj.waw.pl" To: CCL Subject: CCL:G: Question about BSSE in Gaussian Message-Id: <-42401-100801152928-1818-fyV5PdQiWFFbe+owHQy1yg]=[server.ccl.net> X-Original-From: "Marcin Sterniczuk" Date: Sun, 1 Aug 2010 15:29:26 -0400 Sent to CCL by: "Marcin Sterniczuk" [m.sterniczuk..ichtj.waw.pl] Hello, I want compute interaction energy in zeolite system, I want use a Couterpoise method and I have a problem.I define charge and spin in system, "first" part is a zeolite matrix and "second" part is a CO radical molecule. I recived this computation: a) 12 12 12 343 kcal/mol b) 12 01 12 169 kcal/mol c) 12 12 01 15,6 kcal/mol d) 12 343 kcal/mol firs pair is a charge and multiciplity of all system, second the "first" part and a third pair is a "second" part everything is a good with a gaussian help. I recive a corresponding energy for this computation. My system have a 1 charge and 2 spin, if I put charge on a CO molecule (b) I have a 169 kcal/mol, if on zeolite matrix (c) 15,5 kcal/mol. Which posibility I should take to corretly computation? BSSE working correctly for charge system? Please help me. Marcin Sterniczuk Institiute of Nuclear Chemistry and Technology Warsaw/Poland