4. Prepare the membrane system.

Prepare a bilayer membrane system that is consistent with the membrane-embedded protein system. This means using the same kind of water (TP3, OPC…), the same AMBER FF, and the same lipids that are on the membrane (usually only POPC).

The XY size of the box can be of approximately 4 nm (40 Angstroms), which means 24 POPCs per layer. For very large ligands (or peptides), this must be increased, which will only have an effect on the running time.

A standard POPC membrane is provided and can be used. The size of the membrane is 4 nm (XY) and the ions used are Na+ Cl-. If you use this membrane, you can skip to the next section.

4.1. Create the membrane system using CHARMM-GUI.

As in the MEP system (see MEP system), take from the gromacs folder and change the step5_input.gro file name for membrane.gro and the topol.top for membrane.top. Add them to the membrane folder.

The membrane folder should contain at least the following:

membrane
  |  |
  |  |-- toppar
  |  |-- membrane.gro
  |  |-- membrane.top

4.2. Using a different method.

NEMAT searches for the files membrane.top (which references files inside the toppar folder), membrane.gro, and the folder toppar. Therefore, any set of files following this structure is a valid input for NEMAT.

Note

Actually, you could just change a force field folder’s name to toppar and update the #include inside the topology file. This would still provide a valid input for NEMAT.

If you are using a custom force field, it is recommended to use the same for the MEP system.