sorry -- said GAMESS, meant GAUSSIAN.  Well, Jmol takes the orbitals as they come. So use GenNBO files if you want the that sort of NBO order (as far as I know we don't sort them by energy, but I can't say for sure), and use Gaussian if you want standard energy-order.


On Mon, Feb 20, 2012 at 1:36 AM, E.P.A. Couzijn <> wrote:
Dear Jörg,

Actually, I only know about stand-alone NBO5 vs NBO 3.1 as interfaced with Gaussian, but there might be similarities with Gamess.

- The data in the FILE31 -- FILE41 files is sorted as numbered in the NBO output.
  For the NBOs first all bonds are given, followed by all core orbitals, all lone pairs, then all Rydberg states, and finally all antibonds.
  Likewise, NAOs ar sorted by atom number, then angular momentum, then core--valence--Rydberg.
  Thus, it should be very straightforward to find the number of any orbital that you want plotted.

- In Gaussian, with the option SaveNBOs, all NBOs are reordered by their energy for storage in the checkpoint file.
  These energies are listed in the NBO output under "Natural Bond Orbitals (Summary):".
  Furthermore, Gaussian prints the new order (by rows of 10) and the labels of the NBOs (CR/BD/LP/BD*/RY*).
  Thus, one needs to do some counting to get the correct orbital number...

Does the Gamess output give any hint of such a reordering?
If you visualize the first few, do those correspond to core orbitals on the heaviest/most electronegative atoms? That would suggest that they are sorted by energy.

Kind regards,

Dr. Erik P.A. Couzijn
Laboratorium für Organische Chemie
ETH Zürich HCI G 204
CH-8093 Zürich

From: Jörg Saßmannshausen <>
Sent: Saturday, February 18, 2012 11:33 PM
Subject: [Jmol-users] MO numbers in NBO outputfile different from logfile?

Dear all,

I was playing around with a relative 'new' feature of JMOL. I have found out
tonight whilst I was struggling to get some NBO orbitals drawn that JMOL now
can load the output files of the NBO5 program directly instead of loading the
log-file of the calculation. That is great!

However, I am a bit puzzled. If I am loading the log file of a GAMESS
calculation and I issue:
$ frame 1.2; isosurface t2 cutoff 0.05 mo 121 fill translucent 0.5

I get the correct orbital. So far, so good.
However, if I am loading the nbo.31 file and issue the same command, I get a
complete different orbital drawn. Somehow there seems to be no correlation
between the orbital numbers in the log file and the ones in the nbo.31 - nbo.41
files. Is that the way one would expect it? How would I then find out which
orbital number I need to supply when I want to use the nbo.31 - nbo.41 files?

All the best from London!


Jörg Saßmannshausen
University College London
Department of Chemistry
Gordon Street


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