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--- transmembrane_helix_dimers [2025/10/24 09:22] – created admin
+++ transmembrane_helix_dimers [2025/10/24 09:30] (current) – admin
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-Test
+[[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