Created by Nic Kalbaugh and Prof. Jeffery Klauda
Contact email: jbklauda@umd.edu

These instructions are for a simple transmembrane helix dimer setup where one uses protein structure prediction to obtain helix structure. AlphaFold or RCSB structures can be used as well.

Create a COARSE GRAINED model

1. Generate a protein PDB with ROBETTA
2. Get amino acid chain and input into ROBETTA protein prediction software
3. Put in dimer formation: See details in linked Google Doc
4. Build membrane around dimer with CHARMM-GUI Martini Maker
5. A membrane to build should be discussed with your research team or Dr. Klauda. Example listed below is a simple POPC lipid bilayer
6. 15 Å layer of explicit nonpolarizable water at the top and bottom of the system, a bilayer consisting of 100 lipids of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) per leaflet
7. Temperature: 303.15 K
8. Upload it to ZARATAN (your scratch directory)
9. Add your pathway here:
10. Create files inside GROMACS folder to run simulation
11. Analyze Data