CCL:G: Visualize NLMOs from Gaussian output/checkpoint file

 Sent to CCL by: VITORGE Pierre 094605 [Pierre.VITORGE : cea.fr]
 Is it also possible to visualize these orbitals with the last version of
 Molekel?
 Does Molekel 4.3 give correct results? I had some surprises when comparing
 orbitals plotted with Molekel 4.3 and -from gaussian cube file- with VMD.
 --
 Pierre Vitorge
 Directeur de recherche CEA
 Laboratoire Analyse et Modelisation pour la Biologie et l Environnement, LAMBE,
 UMR 8587, CEA, Univ Evry, CNRS,
 Bd. Francois Mitterrand, Bat. Maupertuis, s 02 
 F-91025 Evry, France
 tel.01.69.47.01.40 (+33.1.69.47.01.40)
 pierre.vitorge[]univ-evry.fr
 http://www.lambe.univ-evry.fr/pvitorge
 http://www.vitorge.name
 --
 Laboratoire de Radiolyse et de la Matiere Organique, LRMO (this is the new name
 of the lab.)
 CEA, DEN, Saclay, DPC, SECR, Bat.391 Pe.121
 F-91191 Gif-sur-Yvette, France.
 tel.01.69.08.32.65 (+33.1.69.08.32.65)
 -----Message d'origine-----
 De : owner-chemistry+pierre.vitorge==cea.fr[]ccl.net [mailto:owner-chemistry+pierre.vitorge==cea.fr[]ccl.net] De la part de Jose
 A. Gamez jgamez#%#mpi-muelheim.mpg.de
 Envoyé : vendredi 6 avril 2012 13:15
 À : VITORGE Pierre 094605
 Objet : CCL:G: Visualize NLMOs from Gaussian output/checkpoint file
 Sent to CCL by: "Jose A. Gamez" [jgamez%%mpi-muelheim.mpg.de]
 Dear Wilhelm,
 Here is a small tutorial to visualise NBO related orbitals with molekel4.3 (it
 doesn't work with the last version).
 You can get molekel4.3 from:
 ftp://ftp.cscs.ch/out/molekel/molekel_4.3/
 in the input file add:
 gfoldprint pop=(full,nboread)
 and before the last blank line of the gaussian input, add:
 $NBO PLOT FILE=filename $END
 at the end of your calculation, in addition to the output, you will also have
 eleven filename.[31-41] files. The NLMOs are stored in the filename.39 (you
 can see it in the header of the file), NBOs in filename.38 and so on.
 Now we have to convert the Gaussian09 output (output.log) in something
 understandable for molekel 4.3 (molekel.log), so just run:
 sed "s/Gaussian 09/Gaussian 98/" output.log | sed
 "s/Eigenvalues/EIGENVALUES/g" > molekel.log
 Open molekel, right-button click (keep pressing the button), load -> gaussian
 log and select molekel.log. Once you have your molecule, right-button click,
 load -> nbo orb (remove the filter .orb) and select filename.39. Finally,
 right-button click, compute -> orbital and select the orbital you want to
 visualise.
 I hope this helps. In case you have further questions, feel free to ask me.
 Cheers,
 Jose
 On Thursday 05 April 2012 16:39:30 you wrote:
 > Sent to CCL by: Wilhelm Eger [eger*o*theochem.tu-muenchen.de]
 > Dear all,
 >
 > In order to compare the shapes of a NLMO LP and its parent NBO in regard
 > to delocalization effects, I would like to extract both as a cube file
 >
 > > from a Gaussian calculation.
 >
 > I know the actual procedure consisting of:
 >
 > Run the NBO calculation with the POP=(SaveNBOs) keyword.
 >
 > Transform the resulting checkpoint file to a formatted chechkpoint file
 > using formchk.
 >
 > Look at the end of the calculation output file and get the right
 > position of the desired NBO.
 >
 > Extract the NBO with
 >
 > cubegen 0 mo=X file.fchk MOX.cube -3 h
 >
 > and all other related with
 >
 > cubegen 0 mo=Y file.fchk MOY.cube -3 h MOX.cube
 >
 > to ensure the same dimensions.
 >
 > However, if I run the calculation with POP=(SaveNLMOs), and extract the
 > related MO, I get exactly the same cube files as for the NBO extraction
 > method (e.g. diff results zero). The Gaussian output tells me also of
 > NBOs being stored in the checkpoint file instead of NLMOs. Besides of
 > 'SaveNLMOs' I tried 'SaveMixed' and 'IOP=(6/7=3)', but still the same
 > result. Both G03 and G09 have been used. The desired NBO and NLMO must
 > be different due to significant delocalization of the parent NBO into
 > antibonds.
 >
 > Does anybody know how to reliably extract NLMOs to cube files?
 >
 > Thanks in advance.
 >
 > Regards,
 >
 > Wilhelm
 --
 Dr. Jose A. Gamez
 Max-Planck-Institut für Kohlenforschung
 Kaiser-Wilhelm-Platz 1
 45470 Mülheim an der Ruhr/Germany
   Tel.: +49 208 306 2171http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp-:-//www.ccl.net/chemistry/sub_unsub.shtmlhttp-:-//www.ccl.net/spammers.txt