9.12.1 Amino Acid Protonation and Charge States

How to manually modify protonation and charge states:

Convert your molecule into an ICM Object.
Right click on the residue you want to modify and choose Advanced and choose one of the options from the Set menu .

Options include:

Standard Residue	Alternative Name	Change
CYS	CYM	Deprotonated thiolate: –SH → –S⁻
GLU	GLUH	Protonated glutamic acid: –COO⁻ → –COOH
ASP	ASPH or ASH	Protonated aspartic acid: –COO⁻ → –COOH
LYS	LYN	Neutral lysine: –NH₃⁺ → –NH₂
HIS	HID, HIE or HIP	Proton on Nδ, proton on Nε, or both nitrogens. HIP is positively charged.

The protonation states can be automated using the PROPKA model as described here.

9.12.2 Modify Amino Acid Group

To modify a group:

Convert your molecule into an ICM Object.
Right click on the amino acid residue you wish to modify and choose Edit/Attach Modifier.
Click on the molecular editor icon and use the tools in the molecular editor to sketch the modification you want.
In the molecule editor right click on the atom which will be the attachment point and select "Attachment Point". An asterisk will be placed on that atom.
Close the editor and then click OK in the "Covalently attach a chemical modifier" dialog box (see image above).
Choose to minimize the geometry.