On Tue, Jul 21, 2015 at 5:59 AM, antonio.coluccia.uniroma1.it <
antonio.coluccia.uniroma1.it> wrote:
> Dear amber user's
>
> I would like to visualize the result of the pca analyses on my
> trajectories.
> Following instructions founded at this tutorial :
>
> http://spider.irb.hr/tutorial2/Tutorial2.htm#_B%29_Principal_Component_Analysis
> i was able to produce the covariance matrix and then to compute the
> eigenvector and the eigenvalue. I have obtained that the first two
> eigenvectors share the 70% of the information.
> I have projected the trajectory along the first two PCs obtaining a file
> with mode1 and mode2.
> I this point I would like to visualize the protein movements for both
> the PCs.
>
Then it sounds like what you want is to create a "pseudo-trajectory" along
each of those modes.
This is supported by the modes command that you used below. Just add a
"trajout" argument to it. See page 616 of the Amber 15 manual, with an
example of writing a pseudo-trajectory on page 617.
[snip]
>
>
> center origin :1-982
>
> image origin center
>
I strongly suggest replacing these two commands with the single command
"autoimage"
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 21 2015 - 09:30:02 PDT
