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, BLaDE or domdec_gpu).
Note: water.crd is equilibrated water layer obtained from: https://www.charmm.org/wiki//index.php/CHARMM_Tutorial
For someone not familiar with CHARMM, I think the two important files/directories are:
tutorials and charmm_tutorial_2010.pdf