Hi,
The 'dorotation' keyword for the principal command should do what you want.
Be aware that if you are performing 'dorotation' on a series of structures
(i.e. a trajectory) there may be occasional arbitrary-looking 'flips' of
the structure due to the fact that eigenvectors do not really have a sign.
Although cpptraj has code to try and prevent these flips, they can still
sometimes occur, so you should visually inspect your resulting trajectory
or use a measure like RMSD to ensure the aligned trajectory looks the way
you expect. If you're only aligning one structure this is not an issue of
course.
Hope this helps,
-Dan
On Wed, Feb 26, 2014 at 7:09 AM, Jio M <jiomm.yahoo.com> wrote:
> Hi All,
>
> I want to align molecule longest axis along the z. cpptraj has principal
> axes option but does not tell how much I should rotate?
>
>
> thanks,
> Jiom
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
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 Feb 26 2014 - 07:30:02 PST
