There is also something like
Batch: -r /cwd/receptor_1.pdb -o
/cwd/receptor..pdbqt -A checkhydrogens
sh: 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 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,




Harry Jubb
Part II Biochemistry
Homerton College