Solvate Solvate icon

1gcn in solvent box

Solvate adds solvent around molecule models using AmberTools. Thanks to Wei Zhang for implementing this tool.

Unless already present, hydrogens must be added first. If the molecule model does not include hydrogens, a dialog will appear to allow running AddH before solvent addition.

There are several ways to start Solvate, a tool in the Structure Editing category. It is also implemented as the command solvate.

Models to add solvent to can be chosen from the list with the left mouse button. Ctrl-click toggles the status of an individual model. To choose a block of models without dragging, click on the first (or last) and then Shift-click on the last (or first) in the desired block.

Solvate method options:

The Solvent Model can be any of the following: One can Remove existing ions/solvent (recommended) before solvating the system. OK initiates adding solvent and dismisses the panel, while Apply adds solvent without dismissing the panel. Addition may take several seconds; progress is reported in the status line. Close dismisses the panel without adding any solvent. Help brings up this manual page in a browser window.

See the AmberTools documentation for further details.

UCSF Computer Graphics Laboratory / June 2008