If I modify a PDB file with a specific mutation, how to minimize energy? I have a series of proteins that are all phylogenetically related. Only one of this proteins is currently X-ray crystallized. 

Is it valid to modify the reference PDB file (I mean by hand) to match the mutated sequence? 

And if so, is there any way to minimize the protein energy to find the most likely structure? (Trying to match as closely as possible the reference structure)
Yes you can modify the reference PDB file and look for the changes and for this purpose you need visualizers. One among these is Chimera. You can easily carry out the energy minimization steps using Chimera, first mutate your PDB file manually and then provide it as an input for Chimera and the steps for doing energy minimization are fairly simple as given in Chimera docs here.