Connect with us

Software

How to generate multiple conformers of a ligand using OpenBabel?

Published

on

How to generate multiple conformers of a ligand using OpenBabel?

OpenBabel [1] offers several functions including file format conversion, generation of 3D structures from smiles, and so on. In this article, we are going to generate multiple conformers of a ligand using OpenBabel.

We will use the command-line tool of OpenBabel.

Let’s say, we have an sdf file of a ligand and we want to generate 50 conformers in the same format. Then we will use the following command:

$ obabel -i sdf input.sdf -O conformers.sdf --conformer --nconf 50 --score rmsd --writeconformers

Generating low-energy conformers

If you want to get low-energy conformers for the ligand (input.sdf), then you can use the confab argument. For this, the input file must contain one or more 3D structures. Let’s generate 50 low-energy conformers using the confab argument.

$ obabel input.sdf -O conformers.sdf --confab --conf 50

You can also generate a confab report using the confabreport argument. This argument can also compare the conformers to the reference input structure as shown below:

$ obabel conformers.sdf -oconfabreport -xf input.sdf -xr 1.0

Here, -xr defines the RMSD value within which the conformers are to be compared to the reference (input) structure.

You can generate thousands of conformers depending upon your requirement.


References

  1. O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of cheminformatics3(1), 33.

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