Add Charge


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.

Values for atoms in standard residues (water, standard amino acids, standard nucleic acids, and a few common variants and capping groups) are taken from Amber.
Values for atoms in nonstandard residues (any not classified as standard) are determined using Antechamber, which is included with Chimera.

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.

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):

AMBER ff99SB
AMBER ff99bsc0
AMBER ff02pol.r1
AMBER ff03ua
AMBER ff03
AMBER ff03.r1

Other residues can be handled with either of the following charge calculation methods (details):

AM1-BCC - semi-empirical (AM1) with bond charge correction (BCC)
Gasteiger - faster method based on atom types and connectivity

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):

AMBER ff99SB - charges from all_amino94.lib, all_aminont94.lib, all_aminoct94.lib, all_nucleic94.lib (charges and atom type assignments are unchanged from the original ff99); used when Add Charge is called from Coulombic Surface Coloring or Minimize Structure
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz Jr KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. J Am Chem Soc. 1995 May;117(19):5179-97.
AMBER ff99bsc0 - same charges as ff99SB but uses atom type CI in nucleic acids
Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers. Pérez A, Marchán I, Svozil D, Sponer J, Cheatham TE 3rd, Laughton CA, Orozco M. Biophys J. 2007 Jun 1;92(11):3817-29.
AMBER ff02pol.r1 - charges from all_amino02.lib, all_aminont02.lib, all_aminoct02.lib, all_nucleic02.lib (r1 uses atom type H0 in glycine)
Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation. Cieplak P, Caldwell J, Kollman P. J Comput Chem. 2001 Jul 30;22(10):1048-57.

Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides. Wang ZX, Zhang W, Wu C, Lei H, Cieplak P, Duan Y. J Comput Chem. 2006 Apr 30;27(6):781-90.
AMBER ff03ua - charges from uni_amino03.lib, uni_aminont03.lib, uni_aminoct03.lib, all_nucleic94.lib
New-generation amber united-atom force field. Yang L, Tan CH, Hsieh MJ, Wang J, Duan Y, Cieplak P, Caldwell J, Kollman PA, Luo R. J Phys Chem B. 2006 Jul 6;110(26):13166-76.
This "united-atom" force field treats amino acid sidechain aliphatic hydrogens as if they were collapsed onto the corresponding carbons. All nucleic acid hydrogens and amino acid backbone, polar, and aromatic hydrogens are still explicit. This option generates warning messages about the unrecognized and thus uncharged aliphatic hydrogens, which can be safely ignored.
AMBER ff03 - charges from all_amino03.lib, all_aminont94.lib, all_aminoct94.lib, all_nucleic94.lib
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P. J Comput Chem. 2003 Dec;24(16):1999-2012.
AMBER ff03.r1 - charges from all_amino03.lib, all_aminont03.lib, all_aminoct03.lib, all_nucleic94.lib (r1 uses updated charge sets for N- and C-terminal amino acids)

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:

aspartic acid negative or neutral
- charges for the neutral ASH residue are assigned if one of the carboxylic acid oxygens (preferably OD2 for the proper charge distribution) has atom type O3 and an attached hydrogen
glutamic acid negative or neutral
- charges for the neutral GLH residue are assigned if one of the carboxylic acid oxygens (preferably OE2 for the proper charge distribution) has atom type O3 and an attached hydrogen
cysteine neutral reduced, thiolate (negatively charged), or half-cystine (if there is a disulfide bond)
- charges for the negative CYM residue are assigned if there is no disulfide bond and no atom named HG
lysine positive or neutral
- charges for the neutral LYN residue are assigned if the atom named NZ has atom type N3 and thus two attached hydrogens rather than three
histidine protonated at δ-nitrogen (neutral), ε-nitrogen (neutral), or both (positive)
- in AddH, the histidine protonation states can be user-specified or guessed based on the local environment, and in Coulombic Surface Coloring, they can be user-specified; Add Charge recognizes the state from the presence of hydrogen atom HD1, HE2, or both

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:

editing the input structure file to contain standard atom names that will be recognized
using Dock Prep to perform various fixes on a structure before charge assignment
adding missing atoms with Build Structure
deleting unrecognized atoms that are deemed unnecessary for later calculations
deciding it is acceptable for the unrecognized atoms to have zero charge
assigning charges directly with setattr, defattr, or Define Attribute

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:

AM1-BCC - semi-empirical (AM1) with bond charge correction (BCC), parametrized to reproduce ab initio (HF/6-31G*) electrostatic potentials
Gasteiger - iterative partial equalization of orbital electronegativity

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:

Amber parameter database (Bryce Group, University of Manchester)
REDDB (Université de Picardie Jules Verne and Burnham Institute for Medical Research)

UCSF Computer Graphics Laboratory / March 2009