Automated Set-up of Membrane Proteins Simulations

Go to MemprotMD: http://sbcb.bioch.ox.ac.uk/memprotmd/

This is the home of all membrane protein structures, embedded in lipid bilayers.

1. To browse, click Proteins
2. In the Simple Search box, Search for 4M48
3. Click on the 4M48 image

MemProtViewer - Based on PV (https://biasmv.github.io/pv/)

If WebGL is enabled you should see 'View Molecule'

Click 'VIEW IN BROWSER'

The protein (multi-coloured ribbon) should appear in a grey bilayer.

Manipulation: * Left mouse click and hold to rotate * Middle mouse scroll to zoom in and out. * Hold shift and left mouse click and hold to translate

1. Click the down arrow on the righthand side of the viewer to download the coordinated '4m48-atomistic.pdb'. This should download to either your Downloads or tmp folder depending on the browser.

2. Click the Eye to toggle between Orthoscopic/Perspective

3. Click the Rotate image to change view.

4. You can also enlarge the window to Fullscreen.

Downloading Files

1. In the Downloads section click 'PDB FILES (4)'
2. Click the 'Biological Unit 4m48.pdb'

There is also a link in place for this workshop. Leave this page open. We will will return later in the session.

Setting up a CG simulation

Copy 4m48.pdb to the ~/MemProtMD/Exercises/Ex1 directory and enter this directory.

Remove the non-protein atoms:

grep ATOM 4m48.pdb > 4m48-clean.pdb

Set-up the starting point for the system:

perl ~/MemProtMD/AT2CG/at2cg.pl 4m48-clean.pdb 1 popc

This is the starting system for the simulations.

Enter the MD directory.

cd MD

Within this directory is md.tpr

If you have accessible compute try:

gmx mdrun -deffnm md -v

That sets up a pure bilayer, you can also set up a mixed system using, eg:

perl ~/MemProtMD/AT2CG/at2cg.pl 4m48-clean.pdb 5 popc 40 pope 30 pops 10 pip2 10 chol 10

Go to Exercise 2