Solvate

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:

• 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.

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

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.