[Jmol-users] NBO logfile

[Jörg S. <j.s...@uc...>]

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: j.s...@uc...
web: http://sassy.formativ.net

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