Add Charge

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:

• 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 Amber parameter files all*94.lib.

  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 Amber charge set lacks 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. Note that chain-terminal nucleotide residues will normally have non-integral charges, but the 5' and 3' charges sum to an integer.

  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 setattr (or by editing the structure file) to match atom names in the assignment files
  • editing the assignment files (for example, adding parameters for unrecognized atoms)
  • using Dock Prep to perform various fixes on a structure before charge assignment

  The Amber parameter files include alternative sidechain protonation states for certain residues:

  • aspartic acid negative or neutral
  • glutamic acid negative or neutral
  • cysteine neutral reduced, thiolate (negatively charged), or half-cystine (if there is a disulfide bond)
  • lysine positive or neutral
  • histidine protonated at δ-nitrogen (neutral), ε-nitrogen (neutral), or both (positive)

  AddH will add hydrogens to generate the states shown in bold, although it will not remove any hydrogens that were already present. AddH allows histidine protonation states to be indicated with special residue names or guessed based on the local environment.

  For a variant to be assigned the right set of charges, its protonation state should be corrected before charge assignment by manually deleting any extra hydrogens, adding any missing hydrogens (for example, with Build Structure), or, prior to hydrogen addition, changing atom types with setattr so that the correct number of hydrogens will be added.

• 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:
  • 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.

  Antechamber also determines the gaff types of atoms in nonstandard residues; these are used by Minimize Structure 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.

  Publications involving 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 Actions... Label... other) and are included in subsequently saved Mol2 files.

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).

W.L. Jorgensen, J. Chandrasekhar, and J.D. Madura, "Comparison of simple potential functions for simulating liquid water" J Chem Phys 79:926 (1983).

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

Additional sources of charges and other parameters include:

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