Addcharge is the command-line implementation of Add Charge. It assigns atomic partial charges and Amber/GAFF atom types as the attributes charge and gaffType, respectively. 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.
Charge assignment requires explicit hydrogens, which can be added beforehand with AddH (or the command addh). Structures often have problems such as truncated sidechains that can lead to non-integral net charges. The Dock Prep tool includes options for fixing such problems prior to hydrogen addition and charge assignment.
The keyword std (or s) indicates assignments should only be made to standard residues. If spec is used, the charge assignment will be limited to the entire model(s) containing the specified atoms.
The keyword chargeModel indicates Amber force field version (details):
The keyword nonstd (or n) indicates assignments should only be made to nonstandard residues containing the specified atoms. All of these 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 net-charge for that type of residue must also be supplied; it can be zero, or a positive or negative integer. The charge calculation method can be am1-bcc (default, synonym am1) or gasteiger (synonym gas).
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.
See also: addh, defattr, setattr, minimize, pdb2pqr, Dock Prep, reading charges from files