Hi Daniel
This is indeed a nice suggestion and thanks for support. But I think theoreticaly also its not possible to achieve both at the same time (or its just me who can not think of this being possible theoreticaly!)
In your suggestion, which is a good one, but in the last step the rms fit structures will not be best aligned to Z axis. Its only the reference structure which is best aligned to Z. In summary what I want to say: is it really possible to achieve both things together? I think Not possible, one has to sacrifice one thing!
**********
Just as a note for future searches in archive: I had to split cpptraj commands as it was not outputing trajout:
step1.in
trajin test.inpcrd
principal :1-280 dorotation
trajout test.aligned.rst7
step2.in
reference test.aligned.rst7
trajin test.trj
rms reference mass :1-280
trajout temp.nc
******
On Thursday, February 27, 2014 1:24 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
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)
> _______________________________________________
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 27 2014 - 05:30:03 PST
