Which cpptraj version you are using?
Hai
On Fri, Sep 2, 2016 at 5:38 AM, Anasuya Dighe <anasuya.mbu.iisc.ernet.in>
wrote:
> Dear Amber users,
> I am following the following link by Daniel Roe for carrying out PCA
> analysis :
>
> http://amber.utah.edu/AMBER-workshop/London-2015/pca/pca-cpu-gpu.cpptraj
>
> However, in spite of carrying out each step as shown in the tutorial, I am
> facing an error when I execute these commands one by one on the cpptraj
> terminal
> :
>
> > parm 1abc_water.prmtop [apo]
> > trajin ../1abc_wat_md1.crd.gz parm [apo]
> > rms first :1-246&!.H=
> > average crdset 1abc-average
> > createcrd 1abc-trajectories
> > run
> ---------- RUN BEGIN -------------------------------------------------
>
> PARAMETER FILES:
> 0: [apo] '1abc_water.prmtop', 34832 atoms, 10532 res, box: Orthogonal,
> 10287
> mol, 10281 solvent, 5000 frames
>
> INPUT TRAJECTORIES:
> 0: '1abc_wat_md1.crd.gz' is an AMBER trajectory, Parm [apo] (Orthogonal
> box)
> (reading 5000 of 5000)
> Coordinate processing will occur on 5000 frames.
> TIME: Run Initialization took 0.0000 seconds.
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM '[apo]' (3 actions):
> 0: [rms first :1-246&!.H=]
> Mask [:1-246&!.H*] corresponds to 1963 atoms.
> Mask [:1-246&!.H*] corresponds to 1963 atoms.
> Warning: Coordinates are being rotated and box coordinates are present.
> Warning:
> Unit cell vectors are NOT rotated; imaging will not be possible Warning:
> after
> the RMS-fit is performed.
> 1: [average crdset 1abc-average]
> Averaging over 34832 atoms.
> 2: [createcrd 1abc-trajectories]
> ----- 1abc_wat_md1.crd.gz (1-5000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> Read 5000 frames and processed 5000 frames.
> TIME: Trajectory processing: 130.7463 s
> TIME: Avg. throughput= 38.2420 frames / second.
>
> ACTION OUTPUT:
> AVERAGE: [crdset 1abc-average]
> Writing 'crdset' as Amber Trajectory
> 'crdset' is an AMBER trajectory, Parm [apo]: Writing 5000 frames
> (1-Last, 1)
>
> DATASETS:
> 2 data sets:
> RMSD_00000 "RMSD_00000" (double, rms), size is 5000
> 1abc-trajectories "1abc-trajectories" (coordinates), size is 5000
> (1993 MB) Box
> Coords, 34832 atoms
> ---------- RUN END ---------------------------------------------------
>
> >crdaction 1abc-trajectories rms ref 1abc-average :1-246&!.H=
> Error: Could not get reference with name 1abc-average
>
>
> When I enter the last command, i.e. fitting the frames to the average
> structure,
> I am facing the errror message as shown above. I have already created
> crdset
> 1abc-average, then why isn't cpptraj able to get reference to 1abc-average
> when
> calculating an rms fit ( in the last command ).
>
> Any idea why this is happening? Am I going wrong somewhere?
>
>
> Anasuya
>
>
>
>
>
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Received on Fri Sep 02 2016 - 09:00:02 PDT
