rdock cavity problem

[BL-Lac149597870]

Did you change the reference ligand and protein in cavity.prm when testing different proteins? In your example, I did not see any changes to cavity.prm file and cavity.as file. In rdock documentations, the insertion of the receptor file name and the reference ligand name in cavity.prm file was needed when docking to proteins which means cavity.as file in example_ligand_design folder also need to be changed.

Here is an example of using rdock tools. https://www.cheminformania.com/test-drivin-rdock/