[[bilayer_simulations]]

====== Transmembrane Helix Dimer Build ======

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**

  - Generate a protein PDB with ROBETTA 
  - Get amino acid chain and input into ROBETTA protein prediction software
  - Put in dimer formation: See details in linked [[https://docs.google.com/document/d/13WQH2BWwjVflEQlNCVEERjQso2NNkhAZBOojFRB6CGw/edit?usp=sharing |Google Doc]]
  - Build membrane around dimer with CHARMM-GUI [[https://charmm-gui.org/?doc=input/martini.bilayer|Martini Maker]]
  - A membrane to build should be discussed with your research team or Dr. Klauda. Example listed below is a simple POPC lipid bilayer
  - 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
  - Temperature:  303.15 K
  - Upload it to ZARATAN (your scratch directory)
  - Add your pathway here:
  - Create files inside GROMACS folder to [[https://docs.google.com/document/d/1OllsW1SnsPsm90FXFROFakfOjulrrHN-FuH-O-rOX5I/edit?usp=sharing |run simulation]] 	
  - Analyze Data