Setting up a simunlation for CHARMM

1) Go to the Protein Data Bank (http://www.rcsb.org/pdb/home/home.do) to get PDB file (coordinates)

2) Go to download and find the .pdb you want or search in the top search box. 
Example: 1AKI (http://www.rcsb.org/pdb/explore/explore.do?structureId=1AKi)

3) Download Files -> PDB format

4) Go to CHARMM-GUI: http://www.charmm-gui.org

5) Choose "Input Generator" -> "Quick MD simulator"

6) Upload PDB file (at the bottom) 

7) Pick CHARM for PDB Format 

8) Click Next Step

Make any changes you want, run next step.

9) Go through the steps, making changes as you want. At the end, download the files.

10) Transfer to Kebnekaise (or wherever) and untar, then run with CHARMM after making any changes yourself.