Hi, all My purpose is to get the binding energy by gromacs. I tried to minimize protein-protein docking decoy by using gromacs without water. But after being minimized, the ligand ran away from receptor.
That's not what I expected . I just want to relax the protein-protein interface due to some atom-atom contact crash . By the way, I found the net charge is not zero after adding H atoms on complex by pdb2gmx. Can I solve the non-zero net charge problem by adding H atom on receptor and ligand separately? Any tip is appreciated. Best shiyong
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