Building a protein-detergent complex for an MD simulation

Setting up a simulation system of a protein detergent complex (PDC) can be tedious. To facilitate the required steps, we provide a few scripts that are available for download here.

If you use any of these scripts for a publication, please cite:

Structural properties of protein-detergent complexes from SAXS and MD simulations
Po-chia Chen and Jochen S. Hub
J. Phys. Chem. Lett., 6, 5116–5121 (2015) [www] [pdf] [supporting info]

After unpacking the tar ball, please adapt the line set scriptloc /home/pchen/scripts/micelle-stuff in pack-micelle.tcl, then take a look into example-workflow.bash for a typical workflow. The script demonstrates the setup of a DDM belt around Aquaporin-0 (see images below). Please also take a look at the help text of the Python script, and at the other variables within the VMD script. They will suggest possible adaptations specific to your system.

What you need:

PDC initial

Equilibration:

PDC packed