Hello. We need to prepare our receptor for ensemble docking using prepare_receptor4.py, unfortunately we encountered this error from MolKit:
mgltools/mgltools_x86_64Linux2_1.5.7/MGLToolsPckgs/MolKit/__init__.py", line 21 raise AssertionError as ("%s does't exist") %filename
^ SyntaxError: invalid syntax
We issued the following commands:
export PYTHONPATH=$(pwd)/MGLTools/MGLToolsPckgs/:$PYTHONPATH
python prepare_receptor4.py -r pdb_file -o outputfilename -A checkhydrogens
Attaching the scripts we are using.
Hoping anyone can help us troubleshoot the problem. Thank you.