[sys prep] Gromacs Improvements #5
Description
- unify running with apo vs. holo
- make sure naming and argument ordering is consistent
- better group selection (e.g. Protein_LIG throughout)
- --> auto-renaming Protein -> Protein_LIG in .mdp and .sh files
- new function: auto-run prep
- fix: fix_itp_includes interaction with chains and numbers
- fix: step 04 POSRES Ca renaming
- ??? put input files into lib
- [EXTRA] create a pipeline for more automatic running over many systems