Hi I am very new to PCA analysis.
I am getting an error
Error: # selected coords (8238) != eigenvector size (855)
/: Permission denied.
While using following script, can anyone help e out in solving it?
trajin /projects/chem/ionic/abhi/PRMT7/PRMT7_WT/Analysis/Cluster/new/PRMT7_WT_aMD_0_300ns.crd.gz
rms first :1-344&!.H=
average crdset cpu-gpu-average
createcrd cpu-gpu-trajectories
run
crdaction cpu-gpu-trajectories rms ref cpu-gpu-average :1-344&!.H=
crdaction cpu-gpu-trajectories matrix covar \
name cpu-gpu-covar :1-36&!.H=
runanalysis diagmatrix cpu-gpu-covar out cpu-gpu-evecs.dat \
vecs 3 name myEvecs \
nmwiz nmwizvecs 3 nmwizfile dna.nmd nmwizmask :1-36&!.H=
crdaction cpu-gpu-trajectories projection CPU modes myEvecs \
beg 1 end 3 :1-36&!.H= 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 /projects/chem/ionic/abhi/PRMT7/PRMT7_WT/Analysis/pca/test-3/PRMT7_WT.prmtop
parmstrip !(:1-344&!.H=)
parmwrite out cpu-gpu-modes.prmtop
runanalysis modes name Evecs trajout cpu-gpu-mode1.nc \
pcmin -100 pcmax 100 tmode 1 trajoutmask :1-344&!.H= trajoutfmt netcdf
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Received on Thu Feb 09 2017 - 14:30:02 PST
