Can Vina be used to do small molecules alignment?

[XinheG]

I am trying to use Vina to align ligands, is it possible to do this? I was told it can do alignment really fast, but I didn't find the way.

[rwxayheee]

Hi @XinheG, I don't think Vina does (best-fit) small molecule alignment in basic docking. The printed RMSD are calculated without fitting. If you are looking for an application to perform rigid small molecule alignment, here are a few options: PyMol Align: https://pymolwiki.org/index.php/Align RDKit: https://www.rdkit.org/docs/source/rdkit.Chem.rdMolAlign.html Open 3D Align: https://open3dalign.sourceforge.net/?Home Obabel Obfit: https://openbabel.org/wiki/Obfit