Dear Sir/Madam:
Please help me to solve it as below:
I have several thousand PDB files of complexes.
They have many bump or crash atoms each other between receptor and ligand.
I want to use script or command line to minimize ligand, not receptor.
Using DS with clean Geomery button can't handle several thousand PDB files.
Please help me.
For example as below the link:
http://140.109.55.40/helpds/