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Selection of rotatable bonds in Avogadro

Hi,
can someone tell me, how the number of rotatable bonds in Extensions

Molecular Mechanics >
Conformer Search : Number of Rotatable bonds??? and Number of
conformers??? must be defined

In View > Properties > Bond Properties: The entry Rotatable for the
bonds in the molecule I can not change to Yes

Best greetings

Reinhard Vetter

In View > Properties > Bond Properties: The entry Rotatable for the
bonds in the molecule I can not change to Yes

At the moment, Avogadro directly uses Open Babel’s definitions of possibly rotatable bonds for automated conformer searching.

Several people have legitimately asked about manually setting bonds for conformer searching. I have a basic interface in mind, but haven’t had a chance with a pile of papers and grants to write. If someone were interested, I could talk them through coding.

In short, something along these lines should come in the next few months, but is not yet possible.

Hope that helps,
-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/

I’m also observing this issue. No conformers generated after a conformation search and the number of rotatable bonds displayed as zero for a 44 atom molecule with obvious rotatable bonds (e.g. aliphatic side chain).

And the same results for cyclohexane.

Many conformational tools ignore ring bonds. Efficiently sampling rings is a bit tricky - we’re about to submit a research paper on it, but it will probably be a bit before the code makes it into Avogadro.

In the meantime, you can ring-flip / sample using the auto-optimize tool and pull on atoms to force different conformations.

It would help to know the molecule, file, image, etc. - but I refer to the general comments above.

I downloaded version 1.1 and the conformation search was possible with the same molecules.

While I can understand that’s frustrating, it doesn’t help me identify the issue. If you can post the molecule, image, etc. that would be helpful.