Add Ions adds monatomic counterions around molecule models using AmberTools. Thanks to Wei Zhang (The University of Texas Health Science Center at Houston) for the initial implementation of this tool. See also: Solvate, Write Prmtop
There are several ways to start Add Ions, a tool in the Structure Editing and Amber categories.
The molecule model of interest should be chosen from the list. Multiple models can be chosen, but they will be considered individually rather than as a combined system.
Several Ion types are available. The number of ions can be set to neutralize the structure or to a specific number. To determine whether a positive or negative ion type would be needed to neutralize a structure, one could run AddH and Add Charge (which reports net charge) beforehand.
The ions will be placed in electrostatically favorable locations according to a Coulombic potential on a grid. The molecule model must already include hydrogens and charge assignments; otherwise, dialogs will appear for running AddH and Add Charge as needed prior to adding ions. The potential grid is calculated using a distance-dependent dielectric and ignoring any solvent molecules. A solvent molecule found to overlap with an ion will be removed.
OK initiates adding ions and dismisses the panel, while Apply adds ions without dismissing the panel. Addition may take several seconds; progress is reported in the status line.
Close dismisses the panel without adding any ions. Help brings up this manual page in a browser window.
See the AmberTools addIons documentation for further details.