VFVS post processing erros and questions

Hello VirtualFlow Community!

So, I’ve gotten a lot of things to work and have gotten both tutorials to run, but, am now on the post-processing. By following the tutorial I’m able to get the complete ligand ranking within tutorial 2, however am not able to get all of the information from the vfvs_pp_prepare_dockingposes.sh executable. Specifically, I get this error as an example:

*** Preparing structure PV-001836333248_1_T5 ***
00000/PV-001836333248_1_T5_replica-1.pdbqt
9 molecules converted
9 files output. The first is PV-001836333248_1_T5.rank-1.pdb
==============================
*** Open Babel Error  in ParseParamFile
  Cannot open parameter file
obenergy: could not setup force field.
9 molecules converted
9 files output. The first is PV-001836333248_1_T5.rank-1.sdf
9 molecules converted

I do get a dockingposes.plain directory with all 100 .pdb files and a dockingposes directory that at this path: docking_poses/qvina02_rigid_receptor1/dockingsposes/AABDAE/00000/Z2488677223_13_T1/replica-1
has a list of .pdb and .sdf, a docking.out.pdbqt, and a .energy file. The .energy file has no energies either. Within the pp/dockingposes/qvina02_rigid_receptor directory there are also two files made, compound.energies and compounds.energies.uniq.csv but neither of these files have any energies listed either.

Within my bashrc I have specified paths to openbabel bin and lib locations.

Also, I have used the vfvs_pp_all.sh to perform all post processing, and get the same results.

Anyone have any thoughts?

Cheerfully,
Kirtley

The issues is resolved. Silly me. Didn’t have the datadir path to open babel. Now that I have energies I have an error that stems from open babel. Anyone have any ideas? My thought is that Open Babel is having trouble dealing with bonds between aromatic rings?

 *** Preparing structure PV-001872376050_1_T1 ***
00001/PV-001872376050_1_T1_replica-1.pdbqt
==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is docking.out.pdbqt)