Sidekick software package for automating transmembrane helix simulation
http://sbcb.bioch.ox.ac.uk/Sidekick/
Under Apache license. Check License for details.
Install a version of gromacs into Sidekick_4.5/gromacs. This is available from gromacs.org under its own licence.
https://ftp.gromacs.org/pub/gromacs/
Example of basic usage for a single helix simulation
CG_Helix.py -s GWWLALALALALALALWWA -l 100 -r 5 -t MARTINI_1.1.2.b --special ntermini
On ubuntu bash links to dash- this can be worked around by switching manually with
dkpg-reconfigure dash
Set variable values in HAConf.py to point to your install and data locations
You get a password error if you don't set a stored password- this is legacy (used in Xgrid) and can be generated as below
python2 set_password.py sometext
When configuring locations in conf.plist for batch running, use full path locations (i.e. not ~).