An internal error occurred in ../../../src/lib/parse_pdbqt.cpp(69).

[jianwen350]

Scoring function : vina Rigid receptor: liep.pdbqt Ligand: ligand.pdbqt Grid center: X 15.19 Y 53.903 Z 16.917 Grid size : X 20 Y 20 Z 20 Grid space : 0.375 Exhaustiveness: 32 CPU: 0 Verbosity: 1

An internal error occurred in ../../../src/lib/parse_pdbqt.cpp(69).

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!

[rwxayheee]

Hi @jianwen350 As suggested by the message you posted, can you share your input files and other information?

[jianwen350]

Hi @jianwen350 As suggested by the message you posted, can you share your input files and other information?

Hi @rwxayheee Thanks so much for your reply. The commands I used for preparing ligand and receptor are:

_prepare_receptor4.py -r liep.pdb -o liep4.pdbqt -A hydrogens prepareligand.py -l imb.pdb -o ligand.pdbqt -A hydrogens

As I typed this, error occur: _vina --receptor liep4.pdbqt --ligand ligand.pdbqt --config config.txt --exhaustiveness=32 --out vinaout1.pdbq error: An internal error occurred in ../../../src/lib/parse_pdbqt.cpp(69).

When I use prepare_receptor.py for preparing receptor, a different error occur: _prepare_receptor.py -r liep.pdb -o liep.pdbqt -A hydrogens prepare_ligand4.py -l imb.pdb -o ligand.pdbqt -A hydrogens vina --receptor liep.pdbqt --ligand ligand.pdbqt --config config.txt --exhaustiveness=32 --out vinaout1.pdbq

error: PDBQT parsing error: Atom type 9.00 -17.40 is not a valid AutoDock type (atom types are case-sensitive).

ATOM 1 N MET A 225 19.353 41.547 -3.887 1.00 72.26 -0.263 9.00 -17.40

Thanks so much for helping me. All files I used is attached. bug.zip

[rwxayheee]

Hi @jianwen350

prepare_ligand.py -l imb.pdb -o ligand.pdbqt -A hydrogens

prepare_ligand.py outputs a PDBQ file of the ligand, which is not the expected format for Vina. Compared to a PDBQT file, the PDBQ file is missing the T (the atom type) column.

If you found prepare_ligand.py in a recent version of MGLTools (?), there is a newer version of this python script named prepare_ligand4.py that can make a ligand PDBQT from a ligand PDB file. Take a look at the help messages and the contents of both scripts and you will notice the difference. Let me know if there's anything else i can be of help with

prepare_receptor.py -r liep.pdb -o liep.pdbqt -A hydrogens

Similar problem with prepare_receptor.py - it makes a PDBQS file of the receptor, with S (solvation) but no T (type). At the moment Vina expects both ligand and receptor in the PDBQT format.

You can find more information about the legacy formats in some old manual.