I also want to project PC1 vs PC2 and PC2 vs PC3 as scatter plots if possible
________________________________________
From: Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
Sent: 16 November 2017 12:27:47 PM
To: amber.ambermd.org
Subject: [AMBER] PCA scree plots
Hi Amber users,
I have performed PCA on my MD trajectory of a glycoprotein to investigate glycan motions.
Firstly, I would like to ask if it would be meaningful to calculate the principal motions for the :protein&CA and the :glycans&!.H= separately. The protein is known to hinge
The PCA analysis I performed yesterday was of the :glycoprotein&!.H= and in NMWiz it predominantly shows glycan motions but the porcupines for protein motion makes the output cluttered.
Secondly, which principal component does the .nmd file contain? If it is showing all 3 how can I separate them into a .nmd file for each individual component?
This is my cpptraj script:
trajin traj.nc
rms first :1-720&!.H=
average crdset Ndom_average
createcrd Ndom_trajectories
run
crdaction Ndom_trajectories rms ref Ndom_average :1-720&!.H=
crdaction Ndom_trajectories matrix covar name Ndom_covar :1-720&!.H=
runanalysis diagmatrix Ndom_covar out Ndom_evecs.dat vecs 3 name NdomEvecs nmwiz nmwizvecs 3 nmwizfile Ndom_pca.nmd nmwizmask :1-720&!.H=
crdaction Ndom_trajectories projection Ndom modes NdomEvecs beg 1 end 3 :1-720&!.H= crdframes 1,3000
hist Ndom:1 bins 100 out Ndom_hist.agr norm name Ndom_1
hist Ndom:2 bins 100 out Ndom_hist.agr norm name Ndom_2
hist Ndom:3 bins 100 out Ndom_hist.agr norm name Ndom_3
run
clear all
readdata Ndom_evecs.dat name Evecs
parm NDOM_CPLX_rnb_stripped_box.prmtop
parmstrip !(:1-720&!.H=)
parmwrite out Ndom_modes.prmtop
runanalysis modes name Evecs trajout Ndom_mode1.nc pcmin -100 pcmax 100 tmode 1 trajoutmask :1-720&!.H= trajoutfmt netcdf
runanalysis modes name Evecs trajout Ndom_mode2.nc pcmin -100 pcmax 100 tmode 2 trajoutmask :1-720&!.H= trajoutfmt netcdf
runanalysis modes name Evecs trajout Ndom_mode3.nc pcmin -100 pcmax 100 tmode 3 trajoutmask :1-720&!.H= trajoutfmt netcdf
Lastly, I would like to display the covariance matrix as a heatmap and the PCA results as scree plots. I previously used Bio3D in R but don't have enough RAM for the current MD analysis.
Could these plots be generated in cpptraj from the output of the above script?
Kind regards
Lizelle Lubbe
PhD (Medical biochemistry) candidate
Department of Integrative Biomedical Sciences
University of Cape Town
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Received on Thu Nov 16 2017 - 03:00:02 PST
