Sirs and Madames:
I hope this is the appropriate manner to ask a question about this
software. If this is not, I do apologize; I do not wish to spam.
I would like to search the PES of a molecule of about 40 atoms at the
level of molecular mechanics. Is there a way to see not just the
coordinates and energy of the minimum conformer found, but of all the
examined conformers? i.e., I would like to get maybe the top 10? I
can’t figure out how to get a list of these in an output file.
Robert Molt
molt@qtp.ufl.edu
Bartlett Research Group
Quantum Theory Project
2234 New Physics Bulding #92
PO Box 118435
Gainesville FL 32611-8435
“Nothing is as practical as good theory.”
Robert,
You can do a conformational search by using the Extensions menu … Molecular Mechanics … Conformer Search
If you want, you can select a different Force Field under Extensions … Molecular Mechanics … Setup Force Field
To see the output, go to the View Menu and select Properties … Conformer Properties
Usually you will have to resize the Conformer Properties window to see more than one or two of the listings. Click an entry in the Conformer Properties window to see the structure of that conformer in the main window. I don’t know if there is any simple way to save the results in an output file.
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: Robert Molt [r.molt.chemical.physics@gmail.com]
Sent: Tuesday, September 28, 2010 12:32 AM
To: avogadro-discuss@lists.sourceforge.net
Subject: [Avogadro-Discuss] Question Concerning Conformational Searches
Sirs and Madames:
I hope this is the appropriate manner to ask a question about this software. If this is not, I do apologize; I do not wish to spam.
I would like to search the PES of a molecule of about 40 atoms at the level of molecular mechanics. Is there a way to see not just the coordinates and energy of the minimum conformer found, but of all the examined conformers? i.e., I would like to get maybe the top 10? I can’t figure out how to get a list of these in an output file.
Robert Molt
molt@qtp.ufl.edumailto:molt@qtp.ufl.edu
Bartlett Research Group
Quantum Theory Project
2234 New Physics Bulding #92
PO Box 118435
Gainesville FL 32611-8435
“Nothing is as practical as good theory.”
I would like to search the PES of a molecule of about 40 atoms at the level of molecular mechanics. Is there a way to see not just the coordinates and energy of the minimum conformer found, but of all the examined conformers? i.e., I would like to get maybe the top 10? I can’t figure out how to get a list of these in an output file.
Besides what was said earlier, there is one caveat. The “Weighted Rotor” search (e.g., not-quite official Monte Carlo) only gives the lowest energy conformer right now. I should put that on my “To Do” for the upcoming Open Babel 2.3 release, but it hasn’t been pressing. I think there will be some better techniques in Avogadro in the future.
(If this is something you’d like to do routinely, you should check out the Open Babel code – you can do this from the command-line or from Python or other scripting language and have more control than the Avogadro GUI.)
Best regards,
-Geoff
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/