Simple tools to compute and compare essential dynamics of proteins
Get a bunch of PDB files, assuming they are aligned on each other, and merge them into a single XTC trajectory.
Files can be provided on command line or as a file listing them (to avoid "Argument list too long" bash complaints).
Requires docker to run "my" Gromacs, feel free to change to yours.
Usage:
./mergepdb.sh -o outfile [-l list_of_files] [infiles ...]
Read a topology (PDB, GRO) and trajectory (XTC, TRR, ...) files, strip anything but protein heavy atoms, and calculate essential dynamics coordinates according to Amadei, A. et al, Essential dynamics of proteins, Proteins 17(4):412-24, 1993.
Technically, eigenvalues of the correlation matrix of movements of all the heavy atoms are computed.
Requires numpy and mdtraj.
Output is a sorted numpy array dumped as text.
Usage:
./calc_esd.py -o out.txt -t top.pdb traj.xtc"
Draw graphs of two sets of normalized eigenvalues computed by calc_esd.py. Number of largest eigenvalues to be considered can be secified (all by default).
Requires numpy and matplotlib.
Usage:
./draw_esd.py [-n num] one.txt two.txt