Since you have downloaded the protein structure from PDB without any mutagenesis, then it would be better not to add hydrogen bonds while you are trying to find neighborhood of ligand because eventually during docking when you would be preparing the protein then you would add them, or if you have already added polar bonds to the ligand then there is definitely no need to add any hydrogen bonds to the protein. And there is no need to worry about it because it is not necessary to write about it in your paper once you are able to dock within a specific binding site.
Muniba is a Bioinformatician based in the South China University of Technology. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba