Add Charge Add Charge icon

Add Charge assigns partial charges to atoms. The values are assigned as an atom attribute named charge.

Unless already present, hydrogens must be added prior to charge assignment (for example, with AddH).

There are several ways to start Add Charge, a tool in the Structure Analysis and Structure Editing categories (including using it via Dock Prep). Add Charge is also implemented as the command addcharge.

Models to add charges to 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 and nonstandard residues are treated separately:

Values of the charge attribute can be displayed as atom labels (for example, with Actions... Label... other) and are included in subsequently saved Mol2 files. Besides atomic charges, Add Charge assigns the model attribute named chargeModel the value AMBER99.

Charges in Standard Residues

Standard residues are assigned the charges in the Amber parameter files all*94.lib. These charges, used in the ff94, ff96, ff98, and ff99 versions of the force field, are described in:

W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz, Jr., D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell, and P.A. Kollman, "A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules" J Am Chem Soc 117:5179 (1995).
Water charges correspond to the TIP3P model:
W.L. Jorgensen, J. Chandrasekhar, and J.D. Madura, "Comparison of simple potential functions for simulating liquid water" J Chem Phys 79:926 (1983).
The files used for charge assignment to standard residues are in the share/AddCharge/ directory of a Chimera installation:
  1. amberName.defattr - assigns Amber residue names using the input atom and residue names
  2. charge.defattr - assigns atomic charges using the input atom names and the Amber residue name assignments from the preceding file
Although these are attribute assignment files, only amberName.defattr is used directly. To speed the process, a dictionary file (generated from charge.defattr with the script is used instead of charge.defattr. If charge.defattr is modified, must be run again to generate the corresponding Alternatively, one can assign charges by creating modified copies of these files in any directory and reading them with Define Attribute, but charge assignment will be slower with this approach.

Additional Parameter Sources

Additional sources of charges and other parameters include:

UCSF Computer Graphics Laboratory / January 2008