Principle component analysis (PCA)

We perform PCA using all backbone atom (N,O,C,CA) of the full degradation machinery complex using Cpptraj. Input file is attached below. Then using Normal Model Wizard (NMwiz) plugin in VMD to visualize and observe the essential motion. Specifically, PCA allow us to observe motion by moving your protein along the direction of eigenvector in each eigenmodes. 

Below are input file of performing PCA: 

parm protein.prmtop                           # load your prmtop here
trajin dBET1_r2_400ns_nowat.dcd    # load you trajecotry here
rms first :1-2672@N,O,C,CA              
average crdset cpu-gpu-average
createcrd cpu-gpu-trajectories
run
crdaction cpu-gpu-trajectories rms ref cpu-gpu-average :1-2672@N,O,C,CA
crdaction cpu-gpu-trajectories matrix covar name cpu-gpu-covar :1-2672@N,O,C,CA
runanalysis diagmatrix cpu-gpu-covar out cpu-gpu-evecs.dat vecs 3 name myEvecs nmwiz nmwizvecs 3 nmwizfile dna.nmd nmwizmask :1-2672@N,O,C,CA
crdaction cpu-gpu-trajectories projection CPU modes myEvecs beg 1 end 3 :1-2672@N,O,C,CA crdframes 1,last
hist CPU:1 bins 100 out cpu-gpu-hist.agr norm name CPU-1
hist CPU:2 bins 100 out cpu-gpu-hist.agr norm name CPU-2
hist CPU:3 bins 100 out cpu-gpu-hist.agr norm name CPU-3
run
clear all
readdata cpu-gpu-evecs.dat name Evecs
parm md_c4_dbet1_35.prmtop
parmstrip !(:1-2672@N,O,C,CA)
parmwrite out dbet1_35-modes.prmtop
runanalysis modes name Evecs trajout dbet1_35-mode1.dcd pcmin -400 pcmax 400 tmode 1 trajoutmask :1-2672@N,O,C,CA
runanalysis modes name Evecs trajout dbet1_35-mode2.dcd pcmin -400 pcmax 400 tmode 2 trajoutmask :1-2672@N,O,C,CA
runanalysis modes name Evecs trajout dbet1_35-mode3.dcd pcmin -400 pcmax 400 tmode 3 trajoutmask :1-2672@N,O,C,CA
quit