Hi Luis Eduardo Hernandez Dominguez ,

if it is only for small ligands many free tools exist there. Naturally, I would promote my own program first:

https://github.com/conradhuebler/curcuma

But there are other tools like

https://github.com/charnley/rmsd

https://github.com/grimme-lab/rmsd-tool

https://github.com/qcuaeh/molalignlib

Regards

Conrad

UCSF Chimera (https://www.cgl.ucsf.edu/chimera/) is another molecular visualization tool with built-in capabilities to calculate RMSD between two ligands. After loading both ligands into Chimera, you can use the 'matchmaker' or 'match' command to calculate RMSD:

match #0 #1

-Replace #0 and #1 with the model numbers of your ligands in Chimera.

You can use discovery studio for this purpose.