Command: addcharge

Usage:
addcharge  residue-spec  [ method  am1-bcc | gasteiger ] [ standardizeResidues  list ]

Usage:
addcharge nonstd  residue-spec   residue-name   net-charge  [ method  am1-bcc | gasteiger ]

Using AmberTools 20, the addcharge command assigns atomic partial charges and Amber/GAFF atom types as the attributes charge and gaff_type, respectively. The corresponding tool is Add Charges. Explicit hydrogens must be present; they can be added beforehand with addh. See also: coulombic, dockprep, troubleshooting charge addition

The main addcharge command works on both standard and nonstandard residues, guessing net charges for the latter. The subcommand addcharge nonstd allows specifying the desired integral net-charge of an individual nonstandard residue type with name residue-name, for which the atomic partial charges will be calculated as detailed below. The scope of either command can be limited with a non-blank residue-spec.

• 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.
  
  
• Certain nonstandard residues can be converted to their corresponding standard residues with the standardizeResidues option, where list is a comma-separated list (without spaces) of one or more of the following residue names:
  • 5BU (bromo-UMP) to U (UMP) – change 5-bromouridine-5'-monophosphate to RNA residue uridine-5'-monophosphate by deleting the bromine atom
  • CSL (methylselenyl-dCMP) to C (CMP) – change 2'-methylselenyl-2'-deoxycytidine-5'-phosphate to RNA residue cytidine-5'-monophosphate by replacing the methylselenyl moiety with an oxygen atom named O2' and adjusting the bond length to 1.430 Å
  • UMS (methylselenyl-dUMP) to U (UMP) – change 2'-methylselenyl-2'-deoxyuridine-5'-phosphate to RNA residue uridine-5'-monophosphate by replacing the methylselenyl moiety with an oxygen atom named O2' and adjusting the bond length to 1.430 Å
  • MSE (selenomethionine) to MET (methionine) – change MSE to MET by changing the selenium atom to a sulfur atom named SD and adjusting the CG-SD and SD-CE bond lengths to 1.81 and 1.78 Å, respectively. If not converted, MSE will still get the same partial charges as MET, but the bond lengths will not be changed.
  The default is all but MSE, namely: 5BU,CSL,UMS
  
  
• ATP, ADP, GTP, GDP, NAD, and NDP are assigned charges from the Amber parameter database.
  
  
• The net charges of other nonstandard residues are guessed by the main addcharge command or specified for a single residue type at a time with the addcharge nonstd subcommand. Monatomic ions are simply assigned their net charges. The remaining nonstandard residues are assigned atomic partial charges and GAFF types by Antechamber, which is included with ChimeraX. The method of charge calculation can be either of the following:
  • am1-bcc (default) – 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.