From owner-chemistry@ccl.net Fri Aug 4 04:44:05 2006 From: "Jens Spanget-Larsen spanget ~ ruc.dk" To: CCL Subject: CCL:G: force constants in the G03 "frequency" output file Message-Id: <-32338-060804044157-16870-S2VkIE+kG5ytNCokejdRiw*server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 04 Aug 2006 10:41:43 +0200 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget ~ ruc.dk] Dear Patrick Pang, your problem with the force constant for dihydrogen is related to the definition of reduced mass for diatomic molecules in Gaussian. For a homonuclear diatomic system like dihydrogen, you would usually define the reduced mass as mH*mH/(mH + mH) = mH/2. But in Gaussian the reduced mass for dihydrogen is taken as twice this value, namely mH = 1.0078, as you see from printout. Hence, the corresponding force constant k must also be twice the usually assumed value. Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget++ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ Patrick Pang skpang,ctimail.com wrote: > Sent to CCL by: "Patrick Pang" [skpang%a%ctimail.com] > I employ UB98/AUG-cc-pVDZ to calculate the hydrogen molecule using G03. After optimizing the geometry, the distance between two hydrogen atoms is 0.7587 angstrom. > > Then I perform the frequency calculation, and the output for the force constant is 11.3961 mDyne/angstrom (1139.61 N/m) extracted from: 1 > SGG > Frequencies -- 4380.8712 > Red. masses -- 1.0078 > Frc consts -- 11.3961 > IR Inten -- .0000 > Atom AN X Y Z > 1 1 .00 .00 .71 > 2 1 .00 .00 -.71 > > The force constant in internal coordinates from the same output file is: > 1 > 1 .365989D+00 > It is equal to 569.81 N/m, and it is a half of the value of 1139.61 N/m. > > I also use the change in potential energy to calculate the force constant. The electronic energy of optimized structure is -1.1707171 hartree. The electronic energy of the structure for -0.01 angstrom (i.e. 0.7587 - 0.01) is -1.1706508 hartree. The electronic energy of the structure for +0.01 angstrom (i.e. 0.7587 + 0.01) is -1.1706527 hartree. Because of the potential energy U = 1/2 k x^2, the average force constant (average of force constants calculated from the average of the force constant for 0 <-> +0.01 angstrom and the force constant for 0 <-> -0.01 angstrom) is 569.82 N/m. It is also a half of the value of 1139.61 N/m. > > I further use the "force" keyword to calculate the internal coodinate force for +0.01 angstrom is -0.006728 hartree/bohr. The internal coodinate force for -0.01 angstrom is +0.007144 hartree/bohr. From the equation F = - k x, the force constant is 570.20 N/m, which is the half of the value of 1139.61 N/m. > > Why there are two different force constant values? > > Thank you for your attention. > > If anyone know the answer, please send to skpang^_^ctimail.com > > Patrick Pang From owner-chemistry@ccl.net Fri Aug 4 05:18:04 2006 From: "matthew john tassell mtassell .. gmail.com" To: CCL Subject: CCL: molecular orbitals in molden Message-Id: <-32339-060804044728-18486-GIGYuCzkC9DeCGTO9S4Nrw++server.ccl.net> X-Original-From: "matthew john tassell" Date: Fri, 4 Aug 2006 04:47:26 -0400 Sent to CCL by: "matthew john tassell" [mtassell:-:gmail.com] hi, just wondering if anyone can help me out. ime trying to view molecular orbitals in molden and so far all i can manage to acheive are wire frame orbitals. what i really want to do is view them in a more conventional way where you have your ball and stick molecule and then a semi transparent molecular orbital around the molecule eg (http://www.cmbi.ru.nl/molden/gallery.html). the traditional style one that you see in textbooks etc. ive been using the P GFINPUT IOP(6/7=1) comand in my imput files as surgested by molden.any help would be very much apreichiated, cheers From owner-chemistry@ccl.net Fri Aug 4 05:53:00 2006 From: "Vlad Cojocaru Vlad.Cojocaru.!A!.eml-r.villa-bosch.de" To: CCL Subject: CCL: generating RNA structures Message-Id: <-32340-060804050952-30455-BxrU6cg4sTiaLT+jOjsmJw!A!server.ccl.net> X-Original-From: Vlad Cojocaru Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Fri, 04 Aug 2006 10:27:23 +0200 MIME-Version: 1.0 Sent to CCL by: Vlad Cojocaru [Vlad.Cojocaru^-^eml-r.villa-bosch.de] Dear Balasubramanian, I am not completely sure what actually you are trying to build.. RNA has pretty diverse folds and I wouldnt think that its wise to do any calculation on RNAs that do not have solved crystal or NMR structures unless this RNA is A-helix ... My advice is first look into the NDB data base and try to find an RNA that is similar to yours ... presumably you know the fold of this RNA .... and then try to adapt your sequence to that RNA... Buldged part meaning how many nucleotides ??? What do you mean by mismatches ???? You mean functional non-Watson-Crick base-pairs??? In RNA I believe one cannot talk about mismatches in the sense one talks about DNA simply because a mismatch implies a altered-functional form ... which is not the case for RNA... All non-WatsonCrick basepairs are part of functional RNA motifs ... If you still want to build non-helical RNA structures, you can look at Davod Case's NAB program or even NAMOT2 I believe can deal with such structures (NAMOT works for DNA for sure .. I didnt try it fro RNA) Best vlad Bala subramanian bala(!)igib.res.in wrote: >Sent to CCL by: "Bala subramanian" [bala]![igib.res.in] >Dear cclers, > >Is there any free software using which i can create unusal RNA structures. I have to construct a structure which has some bulge part in one strand. I tried with insightII but it can generate only standard duplex forms. Also in my RNA there are some mismatches which i couldnt generate with insightII. >thank you, >Balasubramanian >IGIB, >Delhi> > > > > > -- Dr. Vlad Cojocaru EML Research gGmbH Molecular and Cellular Modeling Group Schloss-Wolfsbrunnenweg 33 69118 Heidelberg, Germany Phone: +49-6221-533266 Fax: +49-6221-533298 e-mail: Vlad.Cojocaru*|*eml-r.villa-bosch.de http://projects.villa-bosch.de/mcm/people/cojocaru/ From owner-chemistry@ccl.net Fri Aug 4 21:07:00 2006 From: "Sarom Sok sarom.cluster_._gmail.com" To: CCL Subject: CCL:G: New DFT Functionals for GAMESS-US Message-Id: <-32341-060804185402-27780-peijPlaOKHMmUHtwjNbSiw[A]server.ccl.net> X-Original-From: "Sarom Sok" Date: Fri, 4 Aug 2006 18:54:01 -0400 Sent to CCL by: "Sarom Sok" [sarom.cluster=gmail.com] Greetings, I have added some new functionals to a local version of GAMESS-US. More specifically: X3LYP, PW91 Exchange, PW91 Correlation, BPW91, B3LYP (Gaussian version). If you would like to test out these functionals please send an email to : sarom.cluster:gmail.com All you will receive from me is dftexc.src and sarom.src You will need the full GAMESS source code to compile. These functionals will be in the next production release of GAMESS-US (provided that they are correctly coded). Sarom S. Graduate Student Iowa State University/Ames Laboratory Mark Gordon Research Group sarom.cluster:gmail.com From owner-chemistry@ccl.net Fri Aug 4 21:42:00 2006 From: "Hanneke Jansen hanneke_jansen^-^chiron.com" To: CCL Subject: CCL: COMP: ACS Computers in Chemistry (COMP) 2006 Electronic Elections Message-Id: <-32342-060804142147-12332-c6ioyNUdbtCKRcbcEjUptw * server.ccl.net> X-Original-From: "Hanneke Jansen" Date: Fri, 4 Aug 2006 14:21:46 -0400 Sent to CCL by: "Hanneke Jansen" [hanneke_jansen^^^chiron.com] Dear Colleagues: The Computers in Chemistry (COMP) Division of the ACS invites its members to participate in our first electronic election! The division is moving to electronic balloting, to save money and increase the voting participation of our membership. The election is open to all members of the division that were registered as of July 17th. Please contact me at hanneke_jansen===chiron.com if you are a member and did not receive an invite directly from the COMP secretary (COMP_secretary===yahoo.com) on August 1st. Please include your name and ACS membership number in your email. I will verify that you are on the July 17th member list. Once your membership is confirmed, you will receive the official invite with link to vote from COMP_secretary===yahoo.com. Please note that the election runs through September 15th. Were looking forward to your participation ! Sincerely, Hanneke Jansen Secretary of Computers in Chemistry Division, ACS hanneke_jansen===chiron.com