gkxiao/openbabel_2433

Step to reproduce the OpenBabel PDBQT tree error resulting in re-docking failure.

about openbabel 2433

This is an example to show how to reproduce the PDBQT tree error resulting in redocking failure reported in #2423

Materials

1. ligand to be docked: sti.mol2 or sti.sdf
2. ligand prepared by openbabel from sti.mol2: sti_ob.pdbqt
3. ligand prepared by ADT from sti.mol2: sti_adt.pdbqt
4. Vina docking configure file: dock.conf
5. protein file prepared for docking: protein.pdbqt
6. Cognate ligand: reference.sdf

Step to reproduce re-docking failure

1. use openbabel pdbqt

vina --config dock.conf --ligand sti_ob.pdbqt --out sti_ob_out.pdbqt 

2. use ADT pdbqt

vina --config dock.conf --ligand sti_adt.pdbqt --out sti_adt_out.pdbqt 

3. Visualize the docking poses with cognate ligand (reference.sdf)