Example 2: Biphasic Systems
Example 2: Building Biphasic Systems
Studay system
The original tutorial was to make a heterogeneous biphasic system composed of hydrophobic (cyclohexane) and hydrophilic (water) layers.
Here we are going to use benzene to replace cyclohexane as a demostration of how to use CHARMM-GUI to make a new ligand.
As we covered before, Gromacs simulations require two starting input files for a structure:
- Coordinate file: this can be a Protein Data Bank pdb file, or Gromacs
- Toplogy file: this can be a Gromacs top file
Prepare benzene with CHARMM-GUI
Register a Charmm-GUI account
Go to https://charmm-gui.org/ and register an account.
Model a molecule
Go to Ligand Reader and Modeler to search or create a molecule.