sudheer babu wrote:
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?
that's default. use -lys flag and -arg and -glu and -asp
Pls help me.
Thanks in advance.
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
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