Hi,
The ‘crdset’ keyword is not supported by CPPTRAJ 14. Upgrade to AmberTools
17 or use the GitHub version of CPPTRAJ.
-Dan
On Fri, Jan 19, 2018 at 4:48 AM Dr. MANAS MONDAL <manas.pku.edu.cn> wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Jan 19 2018 - 06:00:04 PST
