Solvate Solvate icon

1gcn in solvent box

Solvate adds solvent around molecule models using AmberTools. Thanks to Wei Zhang for implementing this tool. See also: Add Ions, Write Prmtop

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

The 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.

Solvent addition requires explicit hydrogens. If the molecule model does not include hydrogens, a dialog for running AddH beforehand will appear.

Solvate method options:

The Solvent Model can be any of the following: One can Remove existing ions/solvent (recommended) before solvating the system. Partial charges appropriate for the chosen model will be assigned to the solvent atoms as the attribute named charge.

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 / September 2008