Hi,
You are using an out of date version of cpptraj which does not support
passing frame arguments to 'reftraj'. I recommend you update to
AmberTools13.
-Dan
On Thursday, May 30, 2013, wrote:
> 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 <javascript:;>:
>
> > 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 <javascript:;>:
> >
> >> 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.
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <javascript:;>
> 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) 585-9119 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 30 2013 - 06:00:04 PDT
