Setting basename miss several result files.

[Benstime]

if you run "python run_acpype.py -i ws/ligand.mol2 -b ws/ligand"

[alanwilter]

Hmm... I see what you want to do but, no, -b ws/ligand won't create a folder output inside ws dir.

I'll see if it's worth to change -b option to take a dir path as well.

For the moment, to avoid this issue don't use '/' with -b.

[Benstime]

Thanks. I use python code to copy the "run_acpype.py" to dir where I run. It works!