These files can be used to prepare a protein ligand complex including crystal waters for CHARMM. Then the complexed systems can be solvated, neutralized, minimized, heated. After that MD simulations can be run either with NAMD or CHARMM (including openMM and domdec_gpu).
Note: water.crd is equilibrated water layer obtained from: https://www.charmm.org/wiki//index.php/CHARMM_Tutorial