Path C - Module 25: Solvation & Ion Engineering

Drug binding is influenced by the water molecules in the pocket. In this module, you will learn to place your Mpro-inhibitor complex in a realistic water box with physiological salt concentration.

import molsysmt as msm
from molsysmt import systems

# Load Mpro complex
molsys = msm.convert('pdb:6LU7', to_form='molsysmt.MolSys')

# Solvate with 1.0 nm clearance and 150 mM NaCl
solvated_sys = msm.build.solvate(molsys, box_shape='cubic', clearance='1.0 nm', 
                           ionic_strength='150 mM', neutralization='neutralize')

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