Hi,
A few things seem off here. You're loading in 12 frames total (6 from
each trajectory), yet you're only getting 6 frames total in your
output data. It seems like one of the trajectories didn't load
properly. Look at your cpptraj output for 'Error:' or 'Warning:'
messages.
Also, if you really want to get the RMSD of every frame in
'prod_cen_strip_sol_ion_peptide.mdcrd' to every frame in
'../../extraction_and_centering/prod_cen_strip_sol_ion.mdcrd' you
should use the 'reftraj' option:
trajin prod_cen_strip_sol_ion_peptide.mdcrd 1 6
rms2d out output.dat .N,CA,C,O reftraj
../../extraction_and_centering/prod_cen_strip_sol_ion.mdcrd 1 6
For gnuplot-compatible output substitute 'output.gnu' as your output file name.
-Dan
On Wed, May 29, 2013 at 6:10 AM, <dilrajl.bii.a-star.edu.sg> wrote:
> Thanks Daniel and Niel for your suggestions.
>
> So here is my input script file which is am trying for only 6 frames
> as a test.
>
> trajin prod_cen_strip_sol_ion_peptide.mdcrd 1 6
> trajin ../../extraction_and_centering/prod_cen_strip_sol_ion.mdcrd 1 6
> rms2d rmsout output.dat .N,CA,C,O
>
> and the output is:
>
> #Frame Frame_1 Frame_2 Frame_3 Frame_4 Frame_5 Frame_6
> 1 0.000 0.544 1.295 1.119 1.127 1.109
> 2 0.544 0.000 1.233 0.959 0.981 1.009
> 3 1.295 1.233 0.000 0.556 1.231 1.278
> 4 1.119 0.959 0.556 0.000 1.063 1.050
> 5 1.127 0.981 1.231 1.063 0.000 0.420
> 6 1.109 1.009 1.278 1.050 0.420 0.000
>
> So I believe the bottom left corner or the Upper right corner are the
> RMSD between the frames of the trajectories and the other two boxes
> represent the RMSD values within the frames of the trajectories.
>
> Is that correct?
>
> Well I think I am getting the required data for my analysis. But is
> there anything else I can change do?
>
> Dilraj.
>
> Quoting dilrajl.bii.a-star.edu.sg:
>
>> Dear Amber Users,
>> I have two separate trajectories and I want to
>> compute the RMSD between each frame of the first trajectory with
>> every frame of the second trajectory.
>>
>> Is there any means by which one can do this in ptraj or cpptraj?
>>
>> Or if someone has tried this before, could you please direct in
>> performing this analysis.
>>
>> Thank you.
>> Dilraj.
>
>
>
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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 Wed May 29 2013 - 07:30:03 PDT
