Hi all, thanks for your help and sorry for the late reply. I am on the digest mode, hence it takes a bit longer.
The files are too big to send to email so I put them in the dropbox. I hope you have not problems to download them. I have them compressed as well. I am doing the following: $ zap; load "file:/home/sassy/cpch2ph2zr-isobutene-A-bader-nbo.log" filter "NBO" 519 molecular orbitals in model 1.1 $ isosurface s2 mo 17 fill translucent 0.5 s2 created with cutoff=0.05; number of isosurfaces = 1 isosurface full data range -1.0 to 1.0 with color scheme spanning -1.0 to 1.0 Which basically gives me an orbital of the CH2 bridge. If I do this: $ zap; load "file:/home/sassy/output.31" filter "NBO" 519 molecular orbitals in model 1.1 $ isosurface s2 mo 17 fill translucent 0.5 s2 created with cutoff=0.05; number of isosurfaces = 1 isosurface full data range -1.0 to 1.0 with color scheme spanning -1.0 to 1.0 I get a s-type orbital of one of the aromatic CH. According to the log-file, orbital #17 should be: 17. BD ( 1) C 7- H39 which is correct. For me it appears that the orbitals in the NBO output files have a different labeling than the orbitals in the log file. Please note: I am using the NBO5 version which is for Gaussian03, GAMESS and NWChem. I have included the code in the programs so I do not need to run genNBO which is a bit more inconvenient for me. The problem is that the NBO output files do not contain any information like the SECOND ORDER PERTURBATION THEORY ANALYSIS OF FOCK MATRIX IN NBO BASIS etc. which I need. I think people need to be aware of that. Af for the 'filter "NBO"' from one of the previous coresspondance we had on the list I thought that is no longer needed as jmol realises there are 2 sets of MO and hence reads the NBO ones. Did I get that wrong? Regarding Eric's comment of reordering: As I am using the original NBO5 code I don't think there should be a difference between G03 and GAMESS. The order is as suggested: first core, then bonding, then lone pairs, then antibonding followed by Rydberg. The problem in a nutshell: If I want to look at a particular interaction between say bond17 with LP* 256 I _have_ to use the log file and not the NBO output file as the information about the SECOND ORDER PERTURBATION THEORY ANALYSIS OF FOCK MATRIX IN NBO BASIS does not seem to be in there. I hope that makes sense now. All the best from London Jörg -- ************************************************************* Jörg Saßmannshausen University College London Department of Chemistry Gordon Street London WC1H 0AJ email: [email protected] web: http://sassy.formativ.net Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html ------------------------------------------------------------------------------ Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
