Hi,
The 'principal' command may do what you want. It will align
coordinates along the major principal axis (the Z axis). Here is an
example of commands you could use to use to do this in cpptraj:
parm in.pdb
loadcrd in.pdb Input
crdaction Input principal dorotation
crdout Input out.rotate.pdb
Hope this helps,
-Dan
On Sun, Aug 4, 2013 at 9:28 PM, Vijay Manickam Achari
<vjrajamany.yahoo.com> wrote:
>
>
> Dear sir,
>
> I used third party software to build lipid bilayer. By convention, the long axis for bilayer would be Z-axis. But when I check my lipid bilayer (in pdb) format in VMD it shows, the long axis is X-axis.
>
> Is there any way to make the X axis as a Z-axis in ptraj? or other way to do that?
>
> Regards
> Vijay
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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) 585-9119 (Fax)
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Received on Sun Aug 04 2013 - 21:00:03 PDT
