Sir,

I have Discovery Studio 2.5 and I have docked the small ligands (antibacterial) into protein active site (tRNA) by using the LigandFit protocol. As using the same protocol, I have also docked the standard inhibitor to this protein.

The interaction and scoring of test ligands and reference ligands are same. Then, How can, I predict the RMSD value to validate my docking study(Its step wise procedure). What is the use of RMSD value.

Please clarify me.

If think any other informations which relates with it, please give it also.