I have nearly 100 pdb structures to be energy minimized. I need a tool or script to run multiple energy minimization at a stretch. My actual work is to predict the changes in function of a protein with few mutations. So I m in search of automating this process. This is ligand-protein structure.
Have a look at gromacs (http://www.gromacs.org/). You can either use bash to wrap the gromacs calls (as I did) and batch process the pdbs or you can have a look at one of the wrappers on github. There is a bit of set up to do, but their documentation is quite good.
You may want to consider running some docking or MD simulations if you want to full study the ligand-protein bind over time.
During my Phd I study the effect of single point mutation of a protein structure, and gromacs was my tool of choice.