Dear Mahadev,

Generally, water molecules are not involved in the binding of the substrate or drug. Therefore, they are  deleted to ease in the computations and to clear the binding site from possible water molecules that can distort the search. In some cases they are one or two water molecules which are involved in the binding. These should be kept without removal.

Similarly, some ligands found in the pocket proximity do not have any contribution to the binding, hence, it is advised that these will be removed in order to clear the active site for more efficient calculations.

For more details, please see attached file.

Hoping this will be helpful,

Rafik

Dear Mahadev,

Generally, water molecules are not involved in the binding of the substrate or drug. Therefore, they are  deleted to ease in the computations and to clear the binding site from possible water molecules that can distort the search. In some cases they are one or two water molecules which are involved in the binding. These should be kept without removal.

Similarly, some ligands found in the pocket proximity do not have any contribution to the binding, hence, it is advised that these will be removed in order to clear the active site for more efficient calculations.

For more details, please see attached file.

Hoping this will be helpful,

Rafik

Suppose when we do docking with water molecules and ligand, you will not be able to get the correct binding sites because they are not in the category of amino acids (they are considered as non-standard aminoacids or ligands). some computational tools assume these non standard amino acids as ligands. So you will get the results of interactions of your ligand and protein along with those interactions.

 Thanks to Rafiq sir and all for suggestions.