Add Charge Add Charge icon

Atoms can be labeled to show charge values
with Actions... Label... other or with
commands:   labelopt info charge; label

Add Charge assigns atomic partial charges and Amber/GAFF atom types as the attributes charge and gaffType, respectively.

Atomic partial charges are included in saved Mol2 files. The charges and Amber/GAFF atom types are used by other Chimera tools such as Minimize Structure. Atoms can be labeled with their attribute values using Actions... Label... other or the commands labelopt and label.

See also: AddH, Dock Prep, Minimize Structure, Coulombic Surface Coloring, Add Ions, Write Prmtop

There are several ways to start Add Charge, a tool in the Structure Analysis and Structure Editing categories. Add Charge is also implemented as the command addcharge.

Models to process can be chosen from the list with the left mouse button. Ctrl-click toggles the status of an individual model. To choose a block of models without dragging, click on the first (or last) and then Shift-click on the last (or first) in the desired block.

Standard residues can be assigned parameters from any of the following force fields (details):

Other residues can be handled with either of the following charge calculation methods (details): OK initiates processing and dismisses the dialog, Apply initiates processing without dismissing the dialog, and Close simply dismisses the dialog. Help opens this manual page in a browser window.

AddH will be called as needed to add hydrogens. 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.

If there are any nonstandard residues, a dialog will appear for specifying their net charges. The charge calculation method can be changed at this point, if desired.

If a nucleic acid chain has a 5' terminal phosphate, the user will be asked whether this group should be deleted; otherwise, its atoms will be assigned charges of zero (the charge sets lack parameters for 5' phosphates).

A warning will appear if the name of any atom in a standard residue is not recognized or a model's net charge is not an integer; details will be reported in the Reply Log. Cases of unrecognized atoms in standard residues and/or incorrect net charges should be examined and resolved. Note that chain-terminal nucleotide residues will normally have non-integral charges, but the 5' and 3' charges sum to an integer.

Details for Standard Residues

Atoms in standard residues (water, standard amino acids, standard nucleic acids, and a few common variants and capping groups) are assigned charges and atom types taken from Amber parameter files. Charge model corresponds to force field version (see the Amber documentation for further details):

The parameters include alternative sidechain protonation states for some standard residues. By default, AddH adds hydrogens to generate the states shown in bold below, although it does not remove hydrogens already present. The nondefault states can be attained by deleting hydrogens and/or editing atom types (with setattr or Build Structure) before adding hydrogens: Water charges correspond to the TIP3P model:
Comparison of simple potential functions for simulating liquid water. Jorgensen WL, Chandrasekhar J, Madura JD. J Chem Phys. 1983 Jul 15;79(2):926-35.
Note different solvent charge sets can be obtained using Solvate. Charges previously assigned to solvent atoms by Solvate are not overwritten by Add Charge.

Cases of unrecognized atoms in standard residues and/or incorrect net charges should be examined and resolved. Approaches include:

Nonstandard Residues and Antechamber

Charges and GAFF atom types in nonstandard residues (any not classified as standard) are determined using Amber's Antechamber module, which is included with Chimera.

The available charge calculation methods are:

While both methods are much faster than ab initio calculations, the Gasteiger method is the faster and more approximate of the two. Regardless of which method is chosen, residues that are monatomic ions will simply be assigned their net charges.

Publications involving Antechamber use 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.
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.

Additional Parameter Sources

Additional sources of charges and other parameters include:

UCSF Computer Graphics Laboratory / March 2009