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.

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, Add Charge,