DivScore

A quote from the page:

The DivScore package is intended to be used with AMBER and DivCon for preprocessing biological structures (primarily proteins and small molecules) quick geometry optimization, charge calculation, creating job scripts and streamlining workflow within the PyMOL environment. This package was developed to aid my research and hence works within the confines of assumptions that were necessary for streamlining my workflow. However for those who have access to the AMBER and DivCon, it could potentially be useful since it combines the power of PyMOL with that of AMBER for molecular simulation and DivCon for Quantum Mechanics calculations on large biomolecular systems. An example of the capability of DivScore is that, it can perform a quick minimization of a ligand in the active site of a protein based on the AMBER force field and upload the resulting coordinates into PyMOL for visualization. More examples of things one could do will follow in the examples sections.

Web link: DivScore