Hi,
Check the 'nmwiz' keyword (and related keywords) for the 'diagmatrix'
command (Amber 15 manual page 614); this can help you generate input
that can be read by the NMwiz plugin available with VMD, which can be
used to generate so-called "porcupine plots".
Hope this helps,
-Dan
On Thu, Sep 10, 2015 at 9:30 AM, Lara rajam <lara.4884.gmail.com> wrote:
> Dear Amber
> I would like to to PCA analysis for the protein and the ligand bound
> protein.
> I have gone through the manual. I would like to know how to do the
> porcuppine diagram for the motion of the whole protein and if I am
> interested in doing on particular residue range ( local motion ) how to do
> this with cpptraj
>
> thank you
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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 Sep 16 2015 - 08:30:05 PDT
