Docking score changed after updating open babel.

[ngran1]

I made some changes regarding open babel in my env, and after I run my docking protocol, its docking score and rmsd have changed although no changes have been made regarding the structures. Could it really been that open babel changes influenced changes in docking score, although same things have been used???? I use Python 3.9 version

Thank you

[rwxayheee]

Hi, Can you provide some more information on what you used open babel for, or is it just the python binding that is being used by vina internally? How did you prepare your ligand pdbqt files? Prior to converting the ligand files to pdbqt, did you use open babel for any preprocessing, for example, perceiving bonds?

Since version 3.x and onward, there have been major updates on how open babel perceive bonds. Not sure if that is relevant to your problem. If the bonds are perceived in a different way, you can probably see it from the atom types in the ligand pdbqt files. There are many ways to use open babel with vina. A short description of how you have been using them might be helpful for members watching this repo to help you :)

[JonasLi-19]

could you tell us how you prepare the pdbqt files with open babel before and now?