In pymol auto-dock, the ligands and receptors are prepared by using prepare ligand.py and prepare receptor.py python program. this are in built programs, so my question is after taking the receptor and molecules, do we need to minimize them differently before docking?..if we need to then where i can do the minimization (preferably free source software). i have checked in auto-dock (MGL tools)..where we have to follow the steps and have to do ligands one by one..i want to do all ligand minimization at a time ..can anyone help me regarding this ??
PyMOL/AutoDock does not perform energy minimization of your proteins and ligands. The prepare scripts perform operations such as adding hydrogens, charges, creating poses, etc. but do not minimize energy.
If you have a ligand library to screen with and you did not draw those structures yourself, it is most likely already minimized
It is often debatable if your protein needs energy minimization or not and depends largely on how much you trust your protein structure to be correct (except: you do need it in cases of homology modelling that do not perform it automatically). Note that energy minimization does not always result in better structures.
If you really need to perform energy minimization before docking, you can use UCSF Chimera for this task.
If you would just like to prepare your ligand library in one go instead of for each molecule separately, you can take a look at the virtual screening tutorial on the plugin page.