Obenergy: cannot read input format! obabel: cannot read input format!

Hello VirtualFlow Community!

I’ve sucesfully finished a test run,but during the post processing I am meeting some problems.
The command:
head -n 100 …/…/ranking/qvina02_rigid_receptor1/firstposes.all.minindex.sorted.clean > compounds
creates a list called compounds containing the top 100 docking poses with their respective score.
However, after running
vfvs_pp_prepare_dockingposes.sh …/…/…/output-files/complete/qvina02_rigid_receptor1/results/ meta_collection compounds dockingsposes overwrite
problem occurred:
vftools wrong
get two folders and three files, like this
vftools wrong2
but the dockingsposes.plain is empty. How to alter the command or fix the problem? And how to prepare the input ligands file using this dockingsposes result files to run next flexible docking?
Could you help me?

Dear Vera,

Welcome to the forum :slight_smile:

Which version of OpenBabel have you installed? Possibly it is too old and doesn’t support the pdbqt format yet.


Hi Christoph, I’m sorry I fogot to tell you that I solved this problem, just changed it to 2.3.0.

But now I want to use the result of rigid docking to perform flexible docking, I don’t know how to do it, could you help me? Thank you!