Add Charge assigns partial charges to atoms. The values are assigned
as an atom attribute
Unless already present, hydrogens must be added
prior to charge assignment (for example, with
There are several ways to start
Add Charge, a tool in the Structure Editing category
(including using it via
Add Charge is also implemented as the command
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:
- Charges for standard residues (water, standard amino acids,
standard nucleic acids, and a few common variants and capping groups)
are looked up using assignment files based on the
parameter files all*94.lib.
If any atoms in standard residues are not recognized, a warning will appear
and information on the atoms will be sent to the
Cases of unrecognized atoms in standard residues and/or incorrect net charges
should be examined and resolved. Approaches include:
- deciding it is acceptable for the unrecognized atoms to have zero charge
- deleting unrecognized atoms that are deemed
unnecessary for any downstream calculations
- renaming unrecognized atoms with the command
(or by editing the structure file) to match atom names in the
- editing the assignment files
(for example, adding parameters for unrecognized atoms)
- using Dock Prep
to perform various fixes on a structure before charge assignment
Charges for nonstandard residues, if any,
are calculated using Amber's
Antechamber module (included with Chimera).
A dialog will appear for specifying the formal charge of each nonstandard
residue and which charge calculation method
should be used:
While both methods are much faster than ab initio calculations,
the Gasteiger method is the faster and more approximate of the two.
- AM1-BCC - semi-empirical (AM1) with bond charge correction
(BCC), parametrized to reproduce ab initio (HF/6-31G*)
- Gasteiger - iterative partial equalization of orbital
Antechamber also determines the
of atoms in nonstandard residues; these are used by
to associate the atoms with force field parameters.
It may sometimes be necessary to change the
Chimera atom type
of one or more atoms in a nonstandard residue (before hydrogen addition)
to obtain the desired protonation state.
Antechamber use should cite:
J. Wang, W. Wang, P.A. Kollman, and D.A. Case, "Automatic atom type and
bond type perception in molecular mechanical calculations"
J Mol Graph Model 25:247 (2006).
Values of the charge attribute can be displayed as atom labels
(for example, with
Label... other) and are included in subsequently saved
Charges in Standard Residues
Standard residues are assigned the charges in the
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:
Although these are
assignment files, only amberName.defattr is used directly.
To speed the process, a dictionary file dict.py
(generated from charge.defattr with the script attr2dict.py)
is used instead of charge.defattr.
If charge.defattr is modified, attr2dict.py must be
run again to generate the corresponding
dict.py. Alternatively, one can assign charges by
creating modified copies of these files in any directory and reading them
Attribute, but charge assignment will be slower with this approach.
- amberName.defattr - assigns Amber residue names using
the input atom and residue names
- charge.defattr - assigns atomic charges using the input
atom names and the Amber residue name assignments from the preceding file
Additional Parameter Sources
Additional sources of charges and other parameters include:
UCSF Computer Graphics Laboratory / September 2006