Answer for How do I know which result is better in docking?

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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.