I am going to calculate the binding energy between two proteins, which one of them is post translationally modificated. Is there any way to apply this PTM in pdb file before MD simulation?
Yes, e.g. using Vienna-PTM http://vienna-ptm.univie.ac.at , which allows you to modify the protein PTM and obtain force field parameters (GROMOS 45A3, 54A7 and 54A8) and input files needed to perform MD simulations of the modified proteins using the GROMACS package