There is also something like
Batch: prepare_receptor4.py -r /cwd/receptor_1.pdb -o
/cwd/receptor..pdbqt -A checkhydrogens
sh: prepare_receptor4.py: not found

Dear Lina,

I also encountered this error when using the Autodock 4 plugin. I believe that there is a bug in the script for adding hydrogens; my solution for some structures was to use a different program to add hydrogens (I did this using TRITON http://ncbr.chemi.muni.cz/triton/). Also, if I remember correctly, it is best to ensure there are no underscores in your PDB filenames or selections.

I hope that is of some help,

Best,

Harry

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Harry Jubb
Part II Biochemistry
Homerton College