An internal error occurred in ../../../src/lib/parse_pdbqt.cpp(69). about autodock-vina HOT 3 OPEN

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

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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
prepare_ligand.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 vina_out1.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 vina_out1.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

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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If you found prepare_ligand.py in a recent version of MGLTools (?), there is a newer version of this python script named prepare_ligand4.py that can make a ligand PDBQT from a ligand PDB file.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.

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