Molecular docking by AutoDock

[@pramodm25]

How did you go for command prompt window which you have opened for splitting ligand.pdbqt file? at the end of the video.

[@demirkhan9736]

Why did you accept as 30 ?

[@vineetateotia2184]

How to find rmsd of output poses compared to co crystallized ligand to validate the docking?

[@clchemistry7925]

The validation part of docking is not possible by just Autodock. Additionally Pymole is required for calculation of rmsd.

[@vineetateotia2184]

@@clchemistry7925 Have discovery studio licensed version and used cDocker for docking. Now how do I calculate RMSD in discovery studio? If you have that knowle

[@clchemistry7925]

Yes Fisrt You need to Redock cocrystal ligand Then go to chemistry tab ....there is a option calculate RMSD Click ok and select bound ligand as reference Select all docked poses and click on calculate RMSD for heavy atom

[@clchemistry7925]

The lowest RMSD value indicates the robustness. The value should be within 2 angstrom

[@vineetateotia2184]

@@clchemistry7925 do I need to energy minimise and prepare the cocrystal ligand before redocking, as when I do it the conformation changes a bit, and rmsd results in large value