Solvate

Solvate adds solvent around molecule models using AmberTools. Thanks to Wei Zhang for implementing this tool.

Unless already present, hydrogens must be added first. If the molecule model does not include hydrogens, a dialog will appear to allow running AddH before solvent addition.

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

Models to add solvent to can be chosen from the list with the left mouse button. Ctrl-click toggles the status of an individual model. To choose a block of models without dragging, click on the first (or last) and then Shift-click on the last (or first) in the desired block.

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

See the AmberTools documentation for further details.