Usage:
addcharge std [spec atom-spec]

Usage:
addcharge nonstd atom-spec formal-charge [method calc-method] [gaffType true|false]

Usage:
addcharge [all [spec atom-spec] [method calc-method] [gaffType true|false] ]

Addcharge is the command-line implementation of Add Charge, which assigns partial charges to atoms. The values are assigned as an atom attribute named charge and are included in subsequently saved Mol2 files.

Unless already present, hydrogens must be added prior to charge assignment (for example, with addh).

Standard and nonstandard residues are handled 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).

  Unrecognized atom names and non-integral net charges are reported in the Reply Log; such problems 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.

• Charges for nonstandard residues are calculated using Amber's Antechamber module (included with Chimera; publications involving its use should cite the reference).

The keyword nonstd (or n) indicates charges should only be assigned to the nonstandard residues containing the specified atoms. All of the residues must be of the same type (with the same residue name and containing the same types of atoms connected in the same way). The formal-charge for that type of residue must also be supplied; it can be zero, or a positive or negative integer. The calc-method can be am1-bcc (default, synonym am1) or gasteiger (synonym gas).

The keyword all (or a, or the absence of arguments) indicates charges should be assigned to both standard and nonstandard residues. If atoms are specified, the charge assignment will be limited to the entire model(s) containing the specified atoms. If nonstandard residues are found, a dialog for specifying their formal charges will appear. The calc-method is relevant only to nonstandard residues and can be am1-bcc (default, synonym am1) or gasteiger (synonym gas).

The gaffType option (default true) controls whether the gaff types determined by Antechamber for nonstandard residues will be assigned as an attribute named gaffType. Synonyms for true: True, 1. Synonyms for false: False, 0. Minimize Structure (also implemented as the command minimize) uses the gaffType attribute to associate the atoms with force field parameters.

See also: addh, defattr, setattr, minimize, Add Charge,