Dear AMBER users,
Can you please help me to resolve the following error during CPPTRAJ analysis:
INPUT:
parm free-hhaI-open-struc.prmtop
trajin free-hhaI-open-struc_md_30.nc
list trajin
autoimage
rms first :1-327&.CA
average crdset AVG
createcrd trajectories
run
crdaction trajectories rms ref AVG :1-327&.CA
crdaction trajectories matrix covar \
name covar :1-327&.CA
run
**************************************************************************
OUTPUT:
CPPTRAJ: Trajectory Analysis. V14.25
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
INPUT: Reading Input from file npca.in
[parm free-hhaI-open-struc.prmtop]
Reading 'free-hhaI-open-struc.prmtop' as Amber Topology
[trajin free-hhaI-open-struc_md_30.nc]
Reading 'free-hhaI-open-struc_md_30.nc' as Amber NetCDF
[list trajin]
INPUT TRAJECTORIES:
0: 'free-hhaI-open-struc_md_30.nc' is a NetCDF AMBER trajectory, Parm free-hhaI-open-struc.prmtop (Orthogonal box) (reading 1000 of 1000)
Coordinate processing will occur on 1000 frames.
[autoimage]
AUTOIMAGE: To box center based on center of mass, anchor is first molecule.
[rms first :1-327&.CA]
RMSD: (:1-327&.CA), reference is first frame (:1-327&.CA), with fitting.
[average crdset AVG]
AVERAGE: Averaging over coordinates in mask [*]
Start: 1 Stop: Final frame
Writing averaged coords to [crdset]
[createcrd trajectories]
CREATECRD: Saving coordinates from Top free-hhaI-open-struc.prmtop to "trajectories"
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES:
0: 'free-hhaI-open-struc.prmtop', 58561 atoms, 18117 res, box: Orthogonal, 17791 mol, 17789 solvent, 1000 frames
INPUT TRAJECTORIES:
0: 'free-hhaI-open-struc_md_30.nc' is a NetCDF AMBER trajectory, Parm free-hhaI-open-struc.prmtop (Orthogonal box) (reading 1000 of 1000)
Coordinate processing will occur on 1000 frames.
TIME: Run Initialization took 0.0000 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'free-hhaI-open-struc.prmtop' (4 actions):
0: [autoimage]
Anchor molecule is 1
17790 molecules are mobile.
1: [rms first :1-327&.CA]
Target mask: [:1-327&.CA](327)
Reference mask: [:1-327&.CA](327)
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.
2: [average crdset AVG]
Averaging over 58561 atoms.
3: [createcrd trajectories]
----- free-hhaI-open-struc_md_30.nc (1-1000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 1000 frames and processed 1000 frames.
TIME: Trajectory processing: 1.2050 s
TIME: Avg. throughput= 829.8673 frames / second.
ACTION OUTPUT:
AVERAGE: [crdset AVG]
Writing 'crdset' as Amber Trajectory
'crdset' is an AMBER trajectory, Parm free-hhaI-open-struc.prmtop: Writing 1000 frames (1-Last, 1)
DATASETS:
2 data sets:
RMSD_00000 "RMSD_00000" (double, rms), size is 1000
trajectories "trajectories" (coordinates), size is 1000 (670 MB) Box Coords, 58561 atoms
---------- RUN END ---------------------------------------------------
[crdaction trajectories rms ref AVG :1-327&.CA]
Error: Could not get reference with name AVG
1 errors encountered reading input.
TIME: Total execution time: 1.3946 seconds.
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Received on Fri Jan 19 2018 - 02:00:02 PST
