Solvate Solvate icon

1gcn in solvent box

Solvate adds solvent around molecule models using AmberTools. Thanks to Wei Zhang (The University of Texas Health Science Center at Houston) for implementing this tool.

Solvate is mainly useful for adding solvent to a system before writing a prmtop file for Amber. Although Minimize Structure will use the charges from different water models added with Solvate, it will still use the TIP3P model for the remaining water parameters. 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. The affected atoms are those automatically classified by Chimera as ions and solvent. Partial charges corresponding to the chosen solvent model will be assigned as the attribute named charge to atoms in the existing (if not removed) and newly added solvent residues. The process of solvation may move (translate) the structure.

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 2012