I have to find the 4 Armstrong neighborhood of a ligand. When I take the receptor molecule without adding hydrogen bonds and find 4A nbd of ligand, it gives one result. But when I first add hydrogens to the receptor molecule and then after finding the 4A nbd of ligand, it obviously gives different results. I want to know which one is better ??
Second thing, if I have to find the distance between a ligand and any residue in receptor molecule. Do I have to take the central atom distances or minimum distance between any two atoms of the ligand and receptor molecule can be considered ??
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.