In one of my structure I have to put some water molecule in alternate
confimation with amino acid residues and in another case with ligand.
How do I do it in Phenix.
You just need to make sure the "altloc" identifier in the PDB file is set correctly for the atoms of interest. Currently this requires opening the file in a text editor, but I hope to have a better solution available very soon. The water molecule should have the same altloc as the amino acid residues which you want it to interact with - that is, if you set the altloc for the residues to A, the water also needs to be A. You may want to constrain the occupancies to be the same; see the manual here:
-Nat