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Command: addcharge

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

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.

UCSF Resource for Biocomputing, Visualization, and Informatics / January 2023