Hello everyone,

I am trying to analyse the interaction between a protein and some synthesized compounds. I have drawn the compounds in Argus lab, added the hydrogens and then used them for docking.

The problem is when i compare the ligand pdb file and the complex pdb (receptor and ligand) after the docking, i find most of the hydrogens missing from the ligand. Please point me to the probable reason for this. Will really be grateful. Thank you