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

[Yannlefrancois]

Dear Dr Oleg Trott,

One of my Vina error message asked me to report to you via github. So here is all the information requested by the error message.

Version : AutoDock Vina v1.2.5
Computeur : a debian WSL
command line : nothing
Ligand file : 1.pdbqt
receptor : fftmap_1.pdbqt
no output file
random seed : no random seed was printed

error message :
Scoring function : vina
Rigid receptor: ../fftmap_1.pdbqt
Ligand: 1.pdbqt
Grid center: X 43.63 Y 48.475 Z 14.022
Grid size : X 15 Y 15 Z 15
Grid space : 0.375
Exhaustiveness: 8
CPU: 0
Verbosity: 1

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

Error_yann_lefrancois.zip

I'm currently working on automating my virtual screening campaign, and i'm doing my test run on one of the Enamine library (ive included the sdf file).

Here is how i obtained the 1.pdbqt

I copy pasted the second compound of the SDF file into the 1.sdf

then used open babel to change it to pdb then to pdbqt

obabel -isdf 1.sdf -opdb -O 1.pdb
obabel -ipdb 1.pdb -opdbqt -O 1.pdbqt

If any information is missing let me know.

Best wishes,
Yann

[Yannlefrancois]

further_info.zip

A bit more data,
I ran the docking on all my ligand it fails for most of them, but the one i did not fail are

29 41 53 56 66 114 120 157 229 233

i've added in this second zip all the results as well as the file for all the ligands, the error message is the same everytime

Hope this helps

[rwxayheee]

Hi @Yannlefrancois
The ligands (Ligand_Library/${number}.pdbqt) do not have valid coordinates.
To generate 3D conformers, consider adding 3D coordinates in RDKit, 3D structure generation in obabel or similar software. You may view or try to visualise some of them for a quick check. The ligand PDBQT files have to be at least visualisable to be used for docking.

[Yannlefrancois]

Hi @rwxayheee, Thanks a lot.
I'll be working on that ASAP