Docked ligand problem prepared with Meeko

[isilkajun]

I'm docking the native ligand to the structure with the pdb id 4v64. Regardless of sampling or --local_only options, the connectivity of the ligand changes after docking. One of the rings is breaking. I am able to fix the preparing ligand manually but need to use meeko to make hydrated docking. I'm sharing the prepared ligand and docked ligand with meeko and without meeko.
ligand_problem.tar.gz
.

[diogomart]

Thanks for finding this! Please use option:

--keep_chorded_rings

This will fix it while we work on a permanent solution.

[isilkajun]

It worked using --keep_chorded_rings and --keep_equivalent_rings, thanks.