I want to know what does constrain minimization means. Does it mean Keeping the backbone fixed and just minimizing the side chains? I also want to know that which would be a better option regarding the docking of ligand in the protein. Would it be better that i first perform the molecular dynamics of the protein and dock the ligand in the different confirmation that i obtain after simulation. Or would it be better to first dock the ligand and then perform the simulation (Molecular dynamics) and select the best pose my calculating the binding energy.
constrain minimization means if you want to fix some atoms or a group of atoms in a molecule then you can select and run minimization. and otherwise what you said Keeping the backbone fixed and just minimizing the side chains. this both are applicable in constrain minimization.
Regarding the other point i suggest the docking 1st and then can perform the simulation
Constrains and restrains are two types of "limitations" you can impose on your system. The difference between them is that while a restraint is merely a value that should be respected, and thus can be violated, a constraint must be respected. In your case, constrained minimization means, as rituparna stated, that a group of atoms, usually backbone, is prevented from moving during the simulation/minimization.
As for MD+docking, you are talking about ensemble docking, which is starting from an ensemble of states for your molecules to allow some flexibility. This is mainly useful if your docking software does not allow for intrinsic flexibility during the simulation (i.e. rigid-body docking only). It can be useful to generate a few, not many, conformers and feed them to the docking program. I am not an expert on protein-ligand studies but I would look at the energetics out of the docking before embarking in further simulations.