Solvation

Step by step

1. Set the box

   Cubic (edge 30 Å), rectangular, or padded (10 Å around the solute; chosen automatically when a structure is open). Minimum distance 2.0 Å.

2. Choose the solvent

   The solvent and its model (TIP4P/2005 first for water), its density, or a number of molecules.

3. Add ions

   None, Neutralise, a Concentration (default; salt and mol/L) or Custom counts of cations and anions.

4. Press Solvate

   Packing progress is shown; the result opens as a new structure.

The same without the Studio

Every Studio page calls the same core as the caps command and the caps Python package, so a step you clicked can be repeated in a script.

caps solvate solute.pdb -o solvated.data --padding 10 --solvent water \
    --model TIP4P/2005 --salt NaCl --conc 0.15

import caps
from caps import build

solute = caps.open("solute.pdb")
box = build.solvate(solute, padding=10, solvent="water", salt="NaCl", concentration=0.15)
box.save("solvated.data")

Where to go next

PrepareForce fieldType every atom from SMARTS rules, set charges, fill any missing term and give each part of a composite its own force field.PrepareMinimiseRemove close contacts, compress a low-density cell to its target and relax the box.