Addh is the command-line implementation of AddH, which adds hydrogens to molecule models. See the AddH manual page for more information on methodology, protonation states, and effects on radii.
Option keywords for addh can be truncated to unique strings and their case does not matter. A vertical bar "|" designates mutually exclusive options, and default values are indicated with bold. Synonyms for true: True, 1. Synonyms for false: False, 0.
hbond true|false
Hydrogens are placed based on the types of the existing atoms and to avoid clashes; this option controls whether H-bond formation should also be considered. Considering H-bonds increases calculation time, and the method is still under development. Even when hbond is true, hydrogen positions are not energy-minimized, and a globally optimal network in terms of the number of H-bonds or total H-bonding energy is not necessarily found. Both intra- and inter-model hydrogen bonds are considered, including interactions with models to which hydrogens are not being added (as in FindHBond when the scope of the calculation is set to both).
useHisName true|false
Whether to use residue names for histidine to determine which sidechain nitrogens should be protonated: the δ-nitrogen in residues named HID, the ε-nitrogen in HIE, and both nitrogens in HIP. Residues named HIS will be treated as unspecified, and may end up with either or both sidechain nitrogens protonated. If useHisName is false, all histidine residues will be treated as unspecified regardless of which of the above residue names are used. To specify interactively the protonation state of each histidine, use the AddH graphical interface instead of the command addh.
spec atom-spec
Whether to restrict hydrogen addition to a subset of the open molecule models. Hydrogens will be added to the entire model(s) containing the specified atoms. If atom-spec includes any spaces, it must be enclosed in single or double quote marks. Even when only one model is specified, hydrogen placement can be affected by other models perceived to interact with the specified model. Different submodels of the same model are not considered to interact.