A simple tutorial to build a MARTINI membrane with or without a protein using the INSANE tool. Following the building of the membrane, a short minimization run will be done.
All files are located in the insane_tutorial subdirectory.
You will need:
- The insane.py script (provided)
- The martinize.py script (provided)
- DSSP (provided)
- The MARTINI force-field files (provided)
- A .pdb of your membrane protein (provided)
- VMD, to visualize the structures ! http://www.ks.uiuc.edu/Research/vmd/
- If you want to further do simulations/minimization, GROMACS http://www.gromacs.org/
- Jupyter Notebook, if you hope to open the tutorial, http://jupyter.org/install.html
Insane is published here:
- T.A. Wassenaar, H.I. Ingólfsson, R.A. Böckmann, D.P. Tieleman, S.J. Marrink. Computational lipidomics with insane: a versatile tool for generating custom membranes for molecular simulations. JCTC, 11:2144–2155, doi:2015.10.1021/acs.jctc.5b00209