Hi gmx-users, I want to protonate only HIS residues in my protein , so I gave command like this *pdb2gmx -f protein.pdb -HIS then it asked which number of HIS to protonate, I gave numbers of HIS residues which I want protonate , it ran fine without error, but when I open conf.gro file, along with HISH, LYS also protonating and form LYSH. In input file LYS present like this. Why it happening like this? Pls help me. Thanks in advance.
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