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 - 03:00:02 PDT
