Connect with us

Software

Generating multiple low-energy conformers using Avogadro

Published

on

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].

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

  1. 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 cheminformatics4(1), 1-17.

Further Reading

How to generate multiple conformers of a ligand using OpenBabel?

How to perform virtual screening using Pyrx?

How to install idock on Ubuntu?

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

Software

How to execute matlab from terminal in Ubuntu (Linux)?

Published

on

How to execute matlab from terminal in Ubuntu (Linux)?

While trying to install Matlab [1], it generally gives an error stating “matlab: command not found.”. Here, we provide a solution to this error.

(more…)

Continue Reading

Software

How to install Kpax on Ubuntu (Linux)?

Published

on

How to install Kpax on Ubuntu (Linux)?

Kpax is a bioinformatics program to search and align protein structures [1]. It is currently available for Linux platforms only. In this article, we are going to install the latest version of Kpax (5.1.3) on Ubuntu (Linux). (more…)

Continue Reading

Secondary structure

How to run do_dssp command (mkdssp) in Gromacs 2022?

Published

on

How to run do_dssp command in Gromacs 2022?

In the latest version of GROMACS (2022) [1], there are some issues regarding the gmx do_dssp command. Apparently, this command either does not run displaying a fatal error, or if it runs then it does not read any frame from MD simulation files. In this article, we are going to run the same command for GROMACS 2022. (more…)

Continue Reading

LATEST ISSUE

ADVERT