An internal error occurred in ../../../src/lib/tree.h(101)

[WesleyAC]

I am getting started using AutoDock Vina, trying to check the binding of methylphenidate to the DAT receptor to check that everything is working. I am running into the following error:

$ vina --receptor dat.pdbqt --ligand methylphenidate.pdbqt
AutoDock Vina v1.2.5
#################################################################
# If you used AutoDock Vina in your work, please cite:          #
#                                                               #
# J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli  #
# AutoDock Vina 1.2.0: New Docking Methods, Expanded Force      #
# Field, and Python Bindings, J. Chem. Inf. Model. (2021)       #
# DOI 10.1021/acs.jcim.1c00203                                  #
#                                                               #
# O. Trott, A. J. Olson,                                        #
# AutoDock Vina: improving the speed and accuracy of docking    #
# with a new scoring function, efficient optimization and       #
# multithreading, J. Comp. Chem. (2010)                         #
# DOI 10.1002/jcc.21334                                         #
#                                                               #
# Please see https://github.com/ccsb-scripps/AutoDock-Vina for  #
# more information.                                             #
#################################################################

Output will be methylphenidate_out.pdbqt
Scoring function : vina
Rigid receptor: dat.pdbqt
Ligand: methylphenidate.pdbqt
Grid center: X 0 Y 0 Z 0
Grid size  : X 0 Y 0 Z 0
Grid space : 0.375
Exhaustiveness: 8
CPU: 0
Verbosity: 1



An internal error occurred in ../../../src/lib/tree.h(101). 

Please report bugs through the Issue Tracker on GitHub 
(https://github.com/ccsb-scripps/AutoDock-Vina/issues)., so
that this problem can be resolved. The reproducibility of the
error may be vital, so please remember to include the following in
your problem report:
* the EXACT error message,
* your version of the program,
* the type of computer system you are running it on,
* all command line options,
* configuration file (if used),
* ligand file as PDBQT,
* receptor file as PDBQT,
* flexible side chains file as PDBQT (if used),
* output file as PDBQT (if any),
* input (if possible),
* random seed the program used (this is printed when the program starts).

Thank you!

• the EXACT error message: See above
• your version of the program: AutoDock Vina v1.2.5
• the type of computer system you are running it on: Linux, NixOS 24.05
• all command line options: See above
• configuration file (if used): None used
• ligand file as PDBQT: See below
• receptor file as PDBQT: See below
• flexible side chains file as PDBQT (if used): None used
• output file as PDBQT (if any): None generated
• input (if possible): Not sure what this refers to
• random seed the program used (this is printed when the program starts): This was not printed.

methylphenidate.pdbqt was generated with OpenBabel: obabel -ismiles methylphenidate.smiles -opdbqt -Omethylphenidate.pdbqt . methylphenidate.smiles contained COC(=O)C(c1ccccc1)C1CCCCN1. Link to generated PDBQT files

dat.pdbqt was generated with OpenBabel from the AlphaFold-predicted PDB file (probably not ideal but I just grabbed it because it was simple): obabel AF-Q01959-F1-model_v4.pdb -xr -Odat.pdbqt. Link to generated PDBQT files

My assumption is that my preperation of the PDBQT files is incorrect, but if that's the case, there's still a bug here, as the error message should be something better.

[rwxayheee]

Hi @WesleyAC
The ligand's PDBQT file doesn't have valid 3D coordinates. With obabel, a quick fix would be:
obabel -ismiles methylphenidate.smiles -opdbqt -Omethylphenidate.pdbqt --gen3d
Let us know if that works for you

[WesleyAC]

Ah, that makes complete sense in retrospect! And fixes the issue. Should I close this and open a separate issue to improve the error message?

[rwxayheee]

Hi @WesleyAC
Yes, PR is welcome to the develop branch if you're able to provide some fixes to catch similar problems in ligand PDBQT files. Otherwise, you could leave this open or open an issue. It would be tremendously helpful if we could find out underlying problems with input files (like when angles become zero), skip the instances in batch and/or print useful help messages.