Dear Amber users,
I want to know the atomic fluctuation of my RNA-PROTEIN complex. For this I
have used the following below given input file:
trajin *.crd
center origin :1-258
image origin center
strip :Na+
strip :WAT
rms first .P,O3',O5',C3',C4',C5',CA,C,N
matrix covar name cov.mat out cov.mat.dat
diagmatrix cov.mat out coevecs.dat
run
The result I got is given below:
Eigenvector file: COVAR nmodes 1 width 11
13680 13680
-5.72359 10.53080 -7.47835 -5.96162 10.29766 -7.37368
-5.97738
10.36475 -7.35948 -5.94106 10.33123 -7.32167 -4.73740
11.36013
-8.02395 -5.18068 11.95850 -8.72088 -4.14442 12.20480
-7.02992
-4.25255 12.01021 -6.39008 -3.46822 12.23661 -7.06655
-4.29338
13.29288 -6.85008 -4.05973 13.71168 -6.67361 -4.41960
13.41743
-7.08127 -4.60123 13.76515 -6.53413 -5.35218 14.82710
-6.05663
I am confused which column is for Eigenvalues and which is for
Eigenvectors. Kindly suggest me how to interpret this result.
Thanking You,
Richa
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Received on Fri Jan 22 2016 - 04:30:04 PST
