New to Avogadro...questions

General Discussion
1

Hello all

I am new to using Avogadro and GAMESS (longtime Gaussian user) and am
impressed with what the Avogadro interface.

I apologize in advance that I am not a programmer and cannot assist
with these suggestions. However, I have several questions and
suggestions…

  1. I had to rename the GAMESS output file to *.gamout to get Avogadro
    to read it. [suggestion: reading and parsing the first few lines of
    the output file for the word ‘GAMESS’, ‘Gaussian’, etc., would give
    Avogadro the information it needs to correctly interpret the output
    file.]

  2. Avogadro didn’t report the energy from the GAMESS output in the
    properties dialogue box(?)

  3. Does Avogadro have the ability to draw the orbitals, electron
    density, etc.? I couldn’t find it.

Thanks,
Dr. Roy Jensen
(==========)-----------------------------------------¤
Chemistry, Grant MacEwan University
Room 5-172J, 10700-104 Avenue
Edmonton, AB T5J 4S2
780.633.3915

2

Hi Roy,

I can’t comment on questions 1 and 2, but to view orbitals and surfaces use the Extensions menu and select Create Surfaces … After choosing the options you want click on Calculate to generate the surface.

If you can’t see the surface, use the Display Settings and select the checkbox for Surfaces.

I hope this helps,

Steve

Dr. Steven P. Wathen
Associate Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221

(517) 264-7657
swathen@sienaheights.edu

From: Roy Jensen [JensenRH@MacEwan.ca]
Sent: Thursday, March 04, 2010 12:02 PM
To: avogadro-discuss@lists.sourceforge.net
Subject: [Avogadro-Discuss] New to Avogadro…questions…

Hello all

I am new to using Avogadro and GAMESS (longtime Gaussian user) and am
impressed with what the Avogadro interface.

I apologize in advance that I am not a programmer and cannot assist
with these suggestions. However, I have several questions and
suggestions…

  1. I had to rename the GAMESS output file to *.gamout to get Avogadro
    to read it. [suggestion: reading and parsing the first few lines of
    the output file for the word ‘GAMESS’, ‘Gaussian’, etc., would give
    Avogadro the information it needs to correctly interpret the output
    file.]

  2. Avogadro didn’t report the energy from the GAMESS output in the
    properties dialogue box(?)

  3. Does Avogadro have the ability to draw the orbitals, electron
    density, etc.? I couldn’t find it.

Thanks,
Dr. Roy Jensen
(==========)-----------------------------------------¤
Chemistry, Grant MacEwan University
Room 5-172J, 10700-104 Avenue
Edmonton, AB T5J 4S2
780.633.3915

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3
  1. I had to rename the GAMESS output file to *.gamout to get Avogadro
    to read it.

We do look for “GAMESS” or “Gaussian” in files with “.out” or “.log” extensions. What is the filename you use? Alternatively, what version of Open Babel are you using?

  1. Avogadro didn’t report the energy from the GAMESS output in the
    properties dialogue box(?)

This is a little strange – what version of Avogadro are you using?

  1. Does Avogadro have the ability to draw the orbitals, electron
    density, etc.? I couldn’t find it.

At the moment, Avogadro does not support reading orbitals, electron density from GAMESS – only Gaussian and MOPAC are supported in v1.0. Actually, that’s not quite true – several packages like Q-Chem will write a Gaussian-style fchk file, which will work.

Hope that helps,
-Geoff

Prof. Geoffrey Hutchison
Assistant Professor, Department of Chemistry
University of Pittsburgh
http://hutchison.chem.pitt.edu/
Office: (412) 648-0492