Question regarding function receptor in 'AutoDock.py' about notes HOT 1 CLOSED

When you perform grep ATOM you will be transferring this ATOM 1 O HOH to the new file since this line contains the string "ATOM", thus it is carried over to R.pdb and thus to receptor.pdbqt

My advice is to not use grep here and just do it manually, simply open the protein.pdb file in a plain text editor (not word or office) and remove everything except the atoms you need. Pay attention here! because sometimes ATOM will include HOH (water) and these should be removed, HETATM of none amino acids should also be removed (like ligands or sugars or DNA), but the HETATM of amino acids like MSE for example should be kept! save your new file as R.pdb and then continue normally.

So make sure you know and understand the structure of your protein before and after the changes you are making.

from notes.