VFVS post processing erros and questions

VFTools
#1

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

#2

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)
#3

Hi BKAmos

I have the same problem.
obenergy: could not setup force field.
I can’t get the energy, but I install the openbabel. so the result I have extracted is wrong. you say you resolve this problem, could you please tell me how to resolve it?
thank you

sincerely
SK_zang