Protonation States

To set the protonation states in martinize2, the residues that are to be protonated need to follow either the CHARMM or AMBER forcefield family naming convention for protonated residues (see table below).

forcefield	aminoacid	protnated AA
charmm	GLU	GLUP
charmm	ASP	ASPP
charmm	LYS	LSN
charmm	HIS	HSP
amber	GLU	GLH
amber	ASP	ASH
amber	LYS	LYN
amber	HIS	HIP

In order to change the name of your protonated residue you can use the -mutate flag. For example, to change LYS residue 33 in lysozyme to it's neutral form simply run:

martinize2 -f 1HEL.pdb -x cg.pdb -o topol.top -ff martini3001 -elastic -scfix -cys auto -dssp -ignore HOH -mutate A-LYS33:LSN