Dear Sir or Madam:
Good day!
Recently, I use amber to run Gamd and the trajectory can be successfully generated. But when I analyzed the trajectory , It can only read the first 11 frame and reminded me for:NETCDF ERROR : Input/output error Error: Getting coordinates for frame 12
When I try for another time, It provided the ERROR too ,but reminded me the other frame.NETCDF ERROR : Input/output error
Error: Getting coordinates for frame 20
Please help me to solve this situation. Thank you very much, have a nice weekend!
CPPTRAJ: Trajectory Analysis. V14.25 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_> parm ../../nanobody.prmtopReading '../../nanobody.prmtop' as Amber Topology> trajin ../../06_gamd_1.mdcrdReading '../../06_gamd_1.mdcrd' as Amber NetCDFWarning: Box info present in trajectory 06_gamd_1.mdcrd but not inWarning: associated parm ../../nanobody.prmtopWarning: Setting parm box information from trajectory.> reference ../../nanobody.inpcrdReading '../../nanobody.inpcrd' as Amber Restart'nanobody.inpcrd' is an AMBER restart file, no velocities, Parm ../../nanobody.prmtop (reading 1 of 1)> rms reference out protein.rmsd .CA,C,NReference mask: [.CA,C,N](363) RMSD: (.CA,C,N), reference is reference frame nanobody.inpcrd (.CA,C,N), with fitting.> run---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES: 0: '../../nanobody.prmtop', 1794 atoms, 121 res, box: Trunc. Oct., 1 mol, 50000 frames
INPUT TRAJECTORIES: 0: '06_gamd_1.mdcrd' is a NetCDF AMBER trajectory, Parm ../../nanobody.prmtop (Trunc. Oct. box) (reading 50000 of 50000) Coordinate processing will occur on 50000 frames.
REFERENCE FRAMES (1 total): 0: '../../nanobody.inpcrd', frame 1Active reference frame for masks is 0TIME: Run Initialization took 0.0000 seconds.
BEGIN TRAJECTORY PROCESSING:.....................................................ACTION SETUP FOR PARM '../../nanobody.prmtop' (1 actions): 0: [rms reference out protein.rmsd .CA,C,N]Target mask: [.CA,C,N](363)Warning: Coordinates are being rotated and box coordinates are present.Warning: Unit cell vectors are NOT rotated; imaging will not be possibleWarning: after the RMS-fit is performed.----- 06_gamd_1.mdcrd (1-50000, 1) ----- 0% NETCDF Error: Input/output errorError: Getting coordinates for frame 12
Read 11 frames and processed 11 frames.TIME: Trajectory processing: 34.5661 sTIME: Avg. throughput= 0.3182 frames / second.
ACTION OUTPUT:
DATASETS: 1 data set:RMSD_00000 "RMSD_00000" (double, rms), size is 11
DATAFILES: protein.rmsd (Standard Data File): RMSD_00000---------- RUN END --------------------------------------------------->
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Received on Wed Apr 07 2021 - 05:00:02 PDT
