[AMBER] Mail from "Dr. MANAS MONDAL" <manas.pku.edu.cn>.

From: Dr. MANAS MONDAL <manas.pku.edu.cn>
Date: Fri, 19 Jan 2018 17:48:01 +0800 (GMT+08:00)

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.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 19 2018 - 02:00:02 PST
Custom Search