Usage:
solvate box|oct solvent_model box_size

Usage:
solvate cap solvent_model center radius

Usage:
solvate shell solvent_model thickness

The solvate command adds solvent around molecule models using AmberTools. It is the command-line implementation of Solvate. Thanks to Wei Zhang for adding this command.

Explicit hydrogens are needed for solvent addition. If the molecule model does not include hydrogens, a dialog will appear to allow running AddH before solvent addition.

Deleting any existing solvent and ions and closing other molecule models is recommended before solvate is run.

One of the following methods must be specified:

• box - rectangular box with edges no closer than box_size (Å) to any atom in the solute
• oct - truncated octahedron with edges no closer than box_size (Å) to any atom in the solute
• cap - spherical cap with the specified center and radius (Å). The center can be:
  • a residue identified by the residue ID (starting from 1)
  • an atom identified by a string like ddd.xxx, where ddd is the residue ID and xxx is the name of the atom
• shell - a layer of solvent extending thickness (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
• 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

See also: addh, delete, minimize, Solvate