Hi
Thanks for consideration. I have one confusion. I want to do some analysis on this Z axis aligned structures in a trajectory but the same time these structures should have best overlap. I am confused what I should do first?
a) Option 1: First best fit the structures with some reference (does this rms in cpptraj write traj of these strucutres? not sure though) and align them later along Z axis, But this may cause individual snapshot be shifted somewhat which won't be best fit anymore. Somewhat it should look like this:
trajin test.trj
reference test.inpcrd
rms reference mass :1-280
principal dorotation
trajout temp.trj
b) Option 2: First I do alignment along Z axis and later best rmsd fit but again same problem.
trajin test.trj
principal dorotation
reference test.inpcrd
rms reference mass :1-280
trajout temp.trj
thanks
Jio
On Wednesday, February 26, 2014 3:38 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
Hi,
On Wed, Feb 26, 2014 at 8:27 AM, Jio M <jiomm.yahoo.com> wrote:
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
>
The code will align the eigenvector with the largest eigenvalue along the Z axis. There is currently no option to change this, although that's a good idea and will go on my to-do list.
-Dan
--
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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
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Received on Wed Feb 26 2014 - 08:30:03 PST
