On Fri, Jan 22, 2016 at 7:18 AM, richa anand <richaaanand.gmail.com> wrote:
> 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
>
As I said in my last email (about LIE), combine the "center" and "image"
commands into a single "autoimage" command. Also, you should combine the
"strip" commands into a single command that strips both water and sodium:
autoimage
strip :WAT,Na+
>
> 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.
>
T
he output format for modes datasets are described on pages 614 and 615 of
the Amber15.pdf manual. The section you quoted here is neither the
eigenvectors nor eigenvalues -- it is the average coordinates. The
eigenmodes follow lines of "****", which you can search for in the text.
If the description of the file format in the manual does not help, then
feel free to ask for clarification of the parts you don't understand.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jan 22 2016 - 05:30:05 PST
