Add Charges assigns atomic partial charges and Amber/GAFF atom types as the attributes charge and gaff_type, respectively. The command implementation is addcharge. It may be helpful to run Dock Prep beforehand to fix any truncated amino acid sidechains. See also: Add Hydrogens, coulombic, troubleshooting charge addition
Add Charges can be opened from the Structure Editing section of the Tools menu and manipulated like other panels (more...).
Assign charges to: The atomic model(s) to process should be chosen from the list. Also restrict to selection indicates whether to limit assignment to the currently selected atoms.
OK initiates processing and dismisses the dialog, whereas Cancel simply dismisses the dialog. Help opens this page in the Help Viewer. Explicit hydrogens are required for charge assignment; Add Hydrogens will be called as needed.
While both methods are much faster than ab initio calculations, the Gasteiger method is the faster and more approximate of the two.
Note: Antechamber/GAFF are meant to handle most small organic molecules, but not metal complexes, inorganic compounds, or unstable species such as radicals, and may not work well on highly charged molecules. GAFF allows for parametrization of most organic molecules made of C, N, O, H, S, P, F, Cl, Br and I. Publications using results from Antechamber should cite:
Automatic atom type and bond type perception in molecular mechanical calculations. Wang J, Wang W, Kollman PA, Case DA. J Mol Graph Model. 2006 Oct;25(2):247-60.The GAFF atom types and associated parameters are described online and in:
Development and testing of a general amber force field. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA. J Comput Chem. 2004 Jul 15;25(9):1157-74.
OK initiates processing and dismisses the dialog, whereas Cancel simply dismisses the dialog. Help opens this page in the Help Viewer.
Potentially ambiguous or rare (shifted-pKa) protonation states, especially in binding sites and nonstandard residues, should be verified and corrected before charges are assigned. For example, extra hydrogens can be deleted, and atom types can be edited (before hydrogen addition) with setattr or Build Structure.
An unrecognized atom name in a standard residue will cause an error, and if the net charge of a model is not an integer, a warning will be issued. Cases of unrecognized atoms in standard residues and/or incorrect net charges should be examined and resolved.
Dock Prep allows repairing truncated amino acid sidechains, one common cause of non-integral net charges, before adding hydrogens and charges. Standard residues with missing or extra atoms can be identified in the command line as template-mismatch, for example:
label template-mismatch height 2 color red
Note that chain-terminal nucleotide residues will normally have non-integral charges, but the 5' and 3' charges sum to an integer.
Atoms can be labeled with their partial charges by using the menu (Actions... Label... Atoms... Other... Charge) or the label command, for example:
label ligand atoms attribute charge