Hello,
Searching through the archives, I have found that performing DockPrep in batch mode is quite straightforward:
http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html
I have also noticed that, when working from the GUI, energy minimisation involves a previous DockPrep step.
I would like to perform the energy minimisation of several protein-ligand complexes, can this be easily done in batch mode?
Furthermore, I would also be interested of computing the binding energy both prior and after minimisation (possibly including APBS-computed electrostatic terms...). However, this is of secondary importance as it can be easily achieved with other tools.
Eric Pettersen
UCSF Computer Graphics Lab