06.5 Generating 3D Conformations of Compounds in DataWarrior

6.5 Generating 3D Conformations of Compounds in DataWarrior

If you have designed your own compounds or have retrieved compounds from an online source which did not contain 3D structure conformation data, then you will need to generate these in order to use your compounds in docking experiments.

To generate the minimised energy 3D conformation of your compounds in DataWarrior, click Chemistry, then generate conformers…

This will open the dialog box below, here you can just click ok.

Now you have generated the minimised 3D conformation of all compounds in your dataset, you can view these 3D structures in the detail area (bottom right), and can go ahead and save the dataset as a single sdf for docking (see section 6.4).