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 ~).