Hi,
Just look at what the values of the projection of your initial
coordinates are along those principal components (presumably the first
values in the data sets you used to create your histogram).
-Dan
On Wed, Nov 26, 2014 at 4:07 AM, anu chandra <anu80125.gmail.com> wrote:
> Dear Amber users,
>
> I am working with MD simulation of protein -ligand interaction. In order to
> get information about subtle change in protein while ligand binding, I have
> carried out principal component analysis (PCA). I have also drawn the free
> energy landscape using PC1 and PC2, which came up with five low-energy
> basins. is there a way to identify which basin will be encountered at the
> initial stage of simulation?
>
> Many thanks,
>
> Anu
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Nov 26 2014 - 09:30:02 PST
