Chimera Commands Index

addcharge std [spec atom-spec] [chargeModel version]

addcharge nonstd atom-spec net-charge [method am1 | gas ]

addcharge [all [spec atom-spec] [chargeModel version] [method am1 | gas ]]

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.

Explicit hydrogens are required for adding charges. AddH will be called as needed to add hydrogens.

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