Path D - Module 25: Solvation & Ion Engineering

Ion channels need a specific salty environment. In this module, you will learn to place your channel tetramer in a large water box with a high concentration of KCl to mimic the intracellular fluid. Solvation requires exactly one structure because independently solvated frames can produce different solvent topologies. Select one representative structure with msm.convert(..., structure_indices=index) before solvating an ensemble or trajectory.

import molsysmt as msm
from molsysmt import systems

# Load channel system
molsys = msm.convert('pdb:1K4C', to_form='molsysmt.MolSys')

# Solvate and add 300 mM KCl
solvated_sys = msm.build.solvate(molsys, box_shape='cubic', clearance='1.5 nm', 
                           ionic_strength='300 mM', neutralization='neutralize')

msm.info(solvated_sys, element='entity')