Prep scripts (pre-MD)

all_prep.in: file to automate tleap processing prior to running MD

Analysis scripts

run.avg-struc: Use this to obtain average structure and frame from trajectory closest to average structure
cumulative_average.py: Use this to calculate cumulative average of MMPBSA (output file from -eo flag from AMBER), can be adopted for calculating cumulative average of other things too

Makin pretty pics

-pymol.txt: load into pymol for pretty pics, directions in file