Dear Daniel,
Yes there was mistake on my part the last time, the
number of frames should be 12 and not 6 as I had shown. But that is
corrected now.
The issue I am having right now is that when i use the "reftraj"
option as below in my script:
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
I see that the program does not read only 6 frames but rather the
total number of frames from the second trajectory.
Here is my output log file
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
CPPTRAJ: Trajectory Analysis. V12.4
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
INPUT: Reading Input from STDIN, type "go" to run, "quit" to exit:
> [trajin ../prod_cen_strip_sol_ion_peptide.mdcrd 1 6]
[prod_cen_strip_sol_ion_peptide.mdcrd] contains 50000 frames.
> [rms2d rmsout output.dat .N,CA,C,O reftraj
> ../../extraction_and_centering/prod_cen_strip_sol_ion.mdcrd 1 6]
>
INPUT TRAJECTORIES:
[prod_cen_strip_sol_ion_peptide.mdcrd] is a NetCDF AMBER
trajectory, Parm 0 (reading 6 of 50000)
Coordinate processing will occur on 6 frames.
PARAMETER FILES:
0: ../../../solute.parmtop, 251 atoms, 14 res, no box, 6 frames
REFERENCE COORDS:
No reference coordinates.
No frames defined.
OUTPUT TRAJECTORIES:
No files.
ACTIONS: Initializing 1 actions:
0: [rms2d rmsout output.dat .N,CA,C,O reftraj
../../extraction_and_centering/prod_cen_strip_sol_ion.mdcrd 1 6]
[prod_cen_strip_sol_ion.mdcrd] contains 20000 frames.
RMS2D: Mask [.N,CA,C,O], ref traj prod_cen_strip_sol_ion.mdcrd
(mask [.N,CA,C,O]) 20000 frames output to output.dat
Warning: [rms2d] Not all arguments handled: [ 1 6 ]
BEGIN TRAJECTORY PROCESSING:
.....................................................
PARM [solute.parmtop]: Setting up 1 actions.
0: [rms2d rmsout output.dat .N,CA,C,O reftraj
../../extraction_and_centering/prod_cen_strip_sol_ion.mdcrd 1 6]
----- [prod_cen_strip_sol_ion_peptide.mdcrd] (1-6, 1) -----
0% 20% 40% 60% 80% 100% Complete.
Read 6 frames and processed 6 frames.
ACTION OUTPUT:
RMS2D: Calculating RMSDs between each input frame and each reference
trajectory prod_cen_strip_sol_ion.mdcrd frame (120000 total).
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
DATASETS:
There are no data sets set up for analysis.
DATAFILE OUTPUT:
output.dat: Frame_1 Frame_2 Frame_3 Frame_4 ... Frame_19997
Frame_19998 Frame_19999 Frame_20000
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
I am not sure if I am making a mistake somewhere.
Could you please suggest me.
Thank you,
Dilraj.
Quoting dilrajl.bii.a-star.edu.sg:
> 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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Received on Thu May 30 2013 - 05:30:04 PDT
