From owner-chemistry@ccl.net Mon May 12 06:06:00 2008 From: "Jens Thomas j.m.h.thomas-$-dl.ac.uk" To: CCL Subject: CCL: How convert gamess orbitals to molpro orbitals Message-Id: <-36937-080512060416-9850-7EA6BptAazYmb+2Y0GGhaA[-]server.ccl.net> X-Original-From: Jens Thomas Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 12 May 2008 11:03:14 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Thomas [j.m.h.thomas##dl.ac.uk] Hello, The transfer of data between Quantum Chemistry codes is something that cropped up at a meeting we held looking at chemistry tools a few weeks back. We haven't had the chance to look into this in any depth yet, but we've created a section on the Blue Obelisk wiki to document the different formats and provide information about tools/efforts to convert this sort of data. If you manage to transfer the orbital information from GAMESS to MOLPRO, I'd be most grateful if you could document your experiences on the wiki at: http://blueobelisk.sourceforge.net/wiki/ChemToolsMeet_March_08#Data_formats_in_Quantum_Chemistry Alternatively just send my any information/scripts and I'll put them up there so that others can take advantage of what you may learn. You might also want to take a look at cclib, which I think has the ability to suck orbital information from both GAMESS and MOLPRO and might provide you with the basis for a conversion script: http://cclib.sourceforge.net/wiki/index.php/Main_Page Best wishes, Jens Seth Olsen s.olsen1 * uq.edu.au wrote: > > Sent to CCL by: Seth Olsen [s.olsen1- -uq.edu.au] > > > Hi CCL'ers, > > This is not quite true. ASCII orbitals can be read and written using > the MATROP facility. I recommend to any user of MOLPRO that they > become familiar with this utility and use it often. In principle, the > GAMESS $VEC group could be reformatted to be read in by MOLPRO, though > I have never done this myself. Be aware that MOLPRO reorders the > atoms and that this may cause confusion to those not familiar with it. > > Cheers, > > Seth > > Jim Kress ccl_nospam ~~ kressworks.com wrote: >> Sent to CCL by: "Jim Kress" [ccl_nospam{=}kressworks.com] >> Last time I looked, the following was the case: >> >> 1) GAMESS US does not print MOLPRO orbitals >> >> 2) even if GAMESS US did print MOLPRO orbitals, MOLPRO doesn't offer a >> method for reading them from the input file. >> >> Jim >> >> >> >> >>> -----Original Message----- >>> From: owner-chemistry]|[ccl.net [mailto:owner-chemistry]|[ccl.net] >>> Sent: Friday, May 09, 2008 6:41 AM >>> To: Kress, Jim Subject: CCL: How convert gamess orbitals to molpro >>> orbitals >>> >>> >>> Sent to CCL by: "Lilianna Bryjko" [lb435.]|[.st-andrews.ac.uk] I'm >>> looking for informations if there is any way to convert Gamess (US) >>> orbitals to Molpro orbitals. Does maybe Gamess (US) have the option >>> to print Molpro format orbitals. >>> >>> Lilianna Bryjko >>> University of St Andrews >>> >>> >>> >>> -= This is automatically added to each message by the mailing script >>> =- To recover the email address of the author of the message, please >>> change the strange characters on the top line to the ]|[ sign. You >>> can also>>> >>> Search Messages: http://www.ccl.net/htdig (login: ccl, Password: >>> search)http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- =================================================================== Jens Thomas, email: j.m.h.thomas**dl.ac.uk STFC Daresbury Lab, tel: +44-1925-603849 Warrington, fax: +44-1925-603634 WA4 4AD, UK. http: http://www.cse.scitech.ac.uk =================================================================== From owner-chemistry@ccl.net Mon May 12 09:29:00 2008 From: "Bulumoni Kalita bulumoni||tezu.ernet.in" To: CCL Subject: CCL:G: Frequency calculation with ONIOM using UFF in the low level Message-Id: <-36938-080512074051-8812-OQIVSakfKEaPFZLAj6ouHw:server.ccl.net> X-Original-From: "Bulumoni Kalita" Date: Mon, 12 May 2008 07:40:47 -0400 Sent to CCL by: "Bulumoni Kalita" [bulumoni[]tezu.ernet.in] Dear all, I am facing a problem with the frequency calculation with the ONIOM option in Gaussian 03. I am using molecular mechanics UFF for the low level of calculation and B3LYP/6-31G(d,p) in the high level to check the C-O stretching frequeny of a adsorbed CO molecule in zeolite. I am getting number of negative frequencies upto as high as 1000 cm-1, although C-O stretching frequency is coming in the expected range. Is this result considerable? Or is there any method to get rid of these negative frequencies? Again I have checked a smaller zeolite cluster with B3LYP/6-31+G(d,p):RHF/3-21G, where all the frequencies are found to be positive. But we have limited computational facility to calculate the large zeolite cluster with B3LYP:RHF level. Can anyone please help me in solving the problem. Thanks in advance. Bulumoni Kalita Research Scholar Department of Chemical Sciences Tezpur University Assam, India From owner-chemistry@ccl.net Mon May 12 16:30:01 2008 From: "HAO JIANG jianghao]_[pitt.edu" To: CCL Subject: CCL: Lattice dynamics code for rigid molecules Message-Id: <-36939-080512160848-27293-m/S8ypSUe+Z2Q7cVNtbABQ-$-server.ccl.net> X-Original-From: "HAO JIANG" Date: Mon, 12 May 2008 16:08:44 -0400 Sent to CCL by: "HAO JIANG" [jianghao _ pitt.edu] Dear All, Does anyone know a lattice dyanmics code for rigid molecules that is avaliable in public? Thanks a lot! Hao Jiang Department of Chemistry University of Pittsburgh From owner-chemistry@ccl.net Mon May 12 18:01:00 2008 From: "Geoffrey Hutchison geoffh+\a/pitt.edu" To: CCL Subject: CCL: TDDFT, HOMO, LUMO, Band Gap Message-Id: <-36940-080512113036-18188-03mAG6gF/d1xZLt3CHWgYQ__server.ccl.net> X-Original-From: Geoffrey Hutchison Content-transfer-encoding: 7bit Content-type: text/plain; delsp=yes; format=flowed; charset=US-ASCII Date: Mon, 12 May 2008 10:46:51 -0400 MIME-version: 1.0 (Apple Message framework v919.2) Sent to CCL by: Geoffrey Hutchison [geoffh+^^^pitt.edu] > I am trying to figure out exactly how the first excited state > computed by a TDDFT calculation differs from the difference in > energy between the highest Alpha occupied eigenvalue and the lowest > Alpha virtual eigenvalue. Any help would be greatly appreciated. First of all, it's not always true that the "first" (i.e., lowest energy) excited state from TDDFT is necessarily the most important. One key advantage of excited states computed by TDDFT, CIS, ZINDO, etc. is that you have predictions of the oscillator strength. The lowest energy excitation may be a weak oscillator strength, and thus not very useful for experimental comparisons. Furthermore, you mention alpha orbitals. In any sort of open-shell system, alpha and beta eigenvalues will not match up. One key distinction between HOMO-LUMO orbital energies and TDDFT is that the former are one-electron orbitals of the ground state. In some compounds, the HOMO-LUMO gap (e.g., from experimental electrochemistry, computed orbital energies, whatever) is either spin- forbidden or dipole forbidden -- so the lowest energy transition is not actually from the frontier orbitals. The excitations from TDDFT include linear combinations of the one- electron orbitals. Frequently, this means that any given excitation will incorporate multiple eigenvectors. One word of advice is that DFT (and TDDFT) is best able to handle low-energy excitations. There was further discussion on CCL.net a few years ago: http://www.ccl.net/chemistry/resources/messages/2001/10/15.004-dir/index.html Cheers, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh|,|pitt.edu web: http://hutchison.chem.pitt.edu/ From owner-chemistry@ccl.net Mon May 12 20:33:02 2008 From: "Aleksey Kuznetsov AlexKuznetsov2007:yandex.ru" To: CCL Subject: CCL: TURBOMOLE: how to look for transition states in reactions of gas-phase species with clusters on surface Message-Id: <-36941-080512202850-28943-2shA/bRsWCgR6UiiMBhDUg^-^server.ccl.net> X-Original-From: Aleksey Kuznetsov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 13 May 2008 03:55:36 +0400 MIME-Version: 1.0 Sent to CCL by: Aleksey Kuznetsov [AlexKuznetsov2007[A]yandex.ru] Dear CCL Users, I'm interested in looking for transition states in the reactions of small gas-phase molecules with transition metal clusters (containing 4 atoms) adsorbed on MgO surface, using TURBOMOLE. Could anyone recommend me any papers or other sources describing techniques/methodologies of looking for transition states in such cases? Sorry if the question is somewhat vague. Thank you in advance, Aleksey. ------------------------------------------- Dr. Aleksey Kuznetsov Cherry L. Emerson Center for Scientific Computation Emory University 1515 Dickey Drive Atlanta, GA 30322 USA Phone: (404)727-2381 Email: akuznets,euch4e.chem.emory.edu -------------------------------------------