Dear Daniel
Thanks I noted dorotation but was doing some mistake (I guess may be spellings).How dorotation knows along which (X, Y or Z) to be aligned. Now my molecule aligned, more or less, along Z ('more or less' because its not fully symmterical).
Is Z default, can we change default
thanks
On Wednesday, February 26, 2014 3:12 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
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
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 26 2014 - 07:30:03 PST
