Generating multiple low-energy conformers using Avogadro

In our previous article, we generated multiple conformers using OpenBabel. In this article, we are going to generate multiple low-energy conformers of a ligand using Avogadro [1].

Contents

References Further Reading

Let’s say, we have a pdb file of a ligand (namely, ligand.pdb) and we want to generate 100 conformers in the same format. Follow the steps given below.

Open Avogadro.
Go to File --> Open --> ligand.pdb.
Go to Extensions --> Optimize Geometry.
After optimization, set up a force field. Go to Extensions --> Molecular Mechanics --> Setup Force Field...
Select an appropriate force field and number of steps for optimization. MMFF94 is considered a good force field for organic molecules and UFF is also a good option. We are using default values here.
Click Ok.
Now, let’s search for conformers. Go to Extensions --> Molecular Mechanics --> Conformer Search...
Now, select a search method and enter an appropriate number of conformers. We are going to generate 100 conformers only. If you select the ‘Genetic Algorithm’ search method then select a ‘Scoring Method’ as well.
Click Ok. It will start the search and soon you will get the conformers.

References

Hanwell, M. D., Curtis, D. E., Lonie, D. C., Vandermeersch, T., Zurek, E., & Hutchison, G. R. (2012). Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. Journal of cheminformatics, 4(1), 1-17.