Solvate

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:

Box - rectangular box with edges no closer than Box size (Å) to any atom in the solute
Cap - spherical cap with the specified Cap center and Cap Radius (Å). The center can be:
- a residue identified by a number which is the residue ID
- an atom identified by a string like ddd.xxx, where ddd is the residue ID and xxx is the name of the atom
Oct - truncated octahedron with edges no closer than Oct size (Å) to any atom in the solute
Shell - a layer of solvent extending Shell extent (Å) from the solute. The shell will be irregular in shape since it reflects the contours of the solute.

The Solvent Model can be any of the following:

CHCL3BOX - chloroform
MEOHBOX - methanol
NMABOX - N-methylacetamide
POL3BOX - POL3 water model
QSPCFWBOX - qSPC/Fw water model
SPCBOX - SPC/E water model
SPCFWBOX - SPC/Fw water model
TIP3PBOX - TIP3P water model
TIP3PFBOX - TIP3P/F water model
TIP4PBOX - TIP4P water model
TIP4PEWBOX - TIP4P/Ew water model

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