# Do I need to remove water molecules before protein-ligand docking?

I am going to screen small molecules against a protein target. Do I need to remove all the solvent molecules before performing VLS?

If you are not using implicit solvent, then it depends on the tool used —most require them stripped and re-added. If you do keep them, make sure that the crystallographic water (HOH) has the same residue code as the added water (TP3, WAT etc.).