Sheetal Tresa Fernandes Hi

You should be try superimpose ligand using small molecule superimpose align method in Discovery Studio; and in Maestro you can also superimpose both ligands and get RMSD values.

Dear Sheetal,

Discovery may not be able to give a desired result

If you need RMSD from the docking activity try using MOE for refined RMSD for the docking. The post-calculation data on the DataViewer comes with refined RMSD (rmsd_refine) with other data like docking score (S). Attached herewith is the screenshot from MOE DataViewer showing the rmsd_refine information.

Best regards

To check the RMSD after Autodock4, you can typically analyze the output log file (usually with a .dlg extension) from your docking simulation.

The RMSD values, including cluster RMSD and reference RMSD, are provided in a table within this log file.

I agree with waseem.

During docking by autodock we get the RMSD of prepared ligand but in covrystal ligand superimposed.

To get RMSD value, you have to dock the log file of desired ligand using autodock or pyrx.

agree with fahim the cocrystal ligand further dock with corespondig protein by autodock to get the RMSD with docking score

Gautam Bhardwaj and Fahim Ibna Mustafa

Whenever docking perform with pyrx or autidock vina, it minimises on basis of binding energy that shows the 0.000 RMSD values that included upper bound and lower bound RMSD values.

https://zhanggroup.org/DockRMSD/