When we gave our complex in prodigy for calculating binding free energy after that it will give us result with a structure file.In that structure file the drug’s was broken.In every complex that was happened.why?
Prodigy does not modify the PDB file in principle (no energy minimisation or such).
Could be CONECT statements have been removed and your viewer does not show the molecule properly.
The only output of PRODIGY you want is the prediction affinity.