Tool: Add Charges

Add Charges assigns atomic partial charges and Amber/GAFF atom types as the attributes charge and gaff_type, respectively. The command implementation is addcharge. It may be helpful to run Dock Prep beforehand to fix any truncated amino acid sidechains. See also: Add Hydrogens, coulombic, troubleshooting charge addition

Add Charges can be opened from the Structure Editing section of the Tools menu and manipulated like other panels (more...).

Assign charges to: The atomic model(s) to process should be chosen from the list. Also restrict to selection indicates whether to limit assignment to the currently selected atoms.

• “Standardize” certain residue types – whether to convert the following nonstandard residues to the corresponding standard types:
  • selenomethionine (MSE) → methionine (MET) – change the selenium atom to a sulfur atom named SD and adjust the CG-SD and SD-CE bond lengths to 1.81 and 1.78 Å, respectively
  • bromo-UMP (5BU) → UMP (U) – change 5-bromouridine-5'-monophosphate to RNA residue uridine-5'-monophosphate by deleting the bromine atom
  • methylselenyl-dUMP (UMS) → UMP (U) – replace the methylselenyl moiety with an oxygen atom named O2' and adjust the bond length to 1.430 Å
  • methylselenyl-dCMP (CSL) → CMP (C) – replace the methylselenyl moiety with an oxygen atom named O2' and adjust the bond length to 1.430 Å
  
  
• Standard residues (water, standard amino acids, standard nucleic acids, certain lipids, and a few common variants and capping groups) are assigned charges and types from the recommended force field versions in AmberTools 20:
  • protein: ff14SB (files amino12.lib, aminoct12.lib, aminont12.lib)
  • DNA: OL15 (DNA.OL15.lib)
  • RNA: OL3 (RNA.lib)
  • lipid: lipid17 (lipid17.lib)
  • water: TIP3P (atomic_ions.lib, solvents.lib)
  Their Amber residue names are assigned as the attribute amber_name. See the Amber documentation for further force field details.
  
  
• ATP, ADP, GTP, GDP, NAD, and NDP are assigned charges from the Amber parameter database.

OK initiates processing and dismisses the dialog, whereas Cancel simply dismisses the dialog. Help opens this page in the Help Viewer. Explicit hydrogens are required for charge assignment; Add Hydrogens will be called as needed.

• If other nonstandard residue types are present, another dialog will appear for specifying the Net Charge of each. Initial values are guessed, but can be changed as needed. Names of the form RES1+RES2 indicate covalently bonded residues that will be treated as a single unit, and the net charge is for the combined entity. Monatomic ions are simply assigned their net charges, whereas atomic partial charges and GAFF types for the remaining (multiatomic) nonstandard residues are calculated by Antechamber, which is included with ChimeraX. The method of charge calculation can be either of the following:
  • 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, a faster method based on atom types and connectivity

  While both methods are much faster than ab initio calculations, the Gasteiger method is the faster and more approximate of the two.

  Note: Antechamber/GAFF are meant to handle most small organic molecules, but not metal complexes, inorganic compounds, or unstable species such as radicals, and may not work well on highly charged molecules. GAFF allows for parametrization of most organic molecules made of C, N, O, H, S, P, F, Cl, Br and I. Publications using results from Antechamber 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.

  The 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.

OK initiates processing and dismisses the dialog, whereas Cancel simply dismisses the dialog. Help opens this page in the Help Viewer.

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Troubleshooting Charge Addition

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.

An unrecognized atom name in a standard residue will cause an error, and if the net charge of a model is not an integer, a warning will be issued. Cases of unrecognized atoms in standard residues and/or incorrect net charges should be examined and resolved.

Dock Prep allows repairing truncated amino acid sidechains, one common cause of non-integral net charges, before adding hydrogens and charges. Standard residues with missing or extra atoms can be identified in the command line as template-mismatch, for example:

label template-mismatch height 2 color red

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

Atoms can be labeled with their partial charges by using the menu (Actions... Label... Atoms... Other... Charge) or the label command, for example:

label ligand atoms attribute charge