Hi,
On Wed, Feb 26, 2014 at 9:22 AM, Jio M <jiomm.yahoo.com> wrote:
>
> 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?
>
Essentially you want to optimize Z-axis alignment along with best-fit
overlap - currently there is nothing in cpptraj that will allow you do do
both simultaneously; as you've seen you can get either one or the other.
Probably the best (only?) way to do this with the code now is to align your
reference structure (test.inpcrd) along the z-axis with principal, then use
the aligned reference as your reference for RMSD, e.g.
trajin test.inpcrd
principal dorotation
trajout test.aligned.rst7
run
clear trajin
reference test.aligned.rst7
trajin test.trj
rms reference mass :1-280
trajout temp.nc
Let me know if you have any more questions.
-Dan
>
> 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
>
>
> --
> -------------------------
> 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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> 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)
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Received on Wed Feb 26 2014 - 17:30:04 PST
