CPPTRAJ: Trajectory Analysis. V14.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ Reading 'chain_b_test_stripped.top' as Amber Topology INPUT: Reading Input from file input_file_CLUSTER_1 [trajin strip_mdcrd.nc] Reading 'strip_mdcrd.nc' as Amber NetCDF [loadtraj name MYTRAJ] Saving currently loaded input trajectories as data set with name 'MYTRAJ' [cluster crdset MYTRAJ :1-291@CA,N,C,O mass clusters 10 out cluster_out nofit averagelinkage summary summary_out info Cluster_info repout box2.rep repfmt pdb clusterout cluster.nc clusterfmt netcdf] Warning: No clustering algorithm specified; defaulting to 'hieragglo' CLUSTER: Using coords dataset MYTRAJ, clustering using RMSD (mask [:1-291@CA,N,C,O]), mass-weighted, no fitting Hierarchical Agglomerative: 10 clusters, average-linkage. Cluster # vs time will be written to cluster_out Cluster information will be written to Cluster_info Summary of cluster results will be written to summary_out Cluster trajectories will be written to cluster.nc, format Amber NetCDF Cluster representatives will be written to separate trajectories, prefix (box2.rep), format PDB [go] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: 'chain_b_test_stripped.top', 7584 atoms, 291 res, box: None, 1 mol, 250000 frames INPUT TRAJECTORIES: 0: 'strip_mdcrd.nc' is a NetCDF AMBER trajectory, Parm chain_b_test_stripped.top(reading 250000 of 250000) Coordinate processing will occur on 250000 frames. TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: ----- strip_mdcrd.nc (1-250000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 250000 frames and processed 250000 frames. TIME: Trajectory processing: 648.0897 s TIME: Avg. throughput= 385.7491 frames / second. ACTION OUTPUT: ANALYSIS: Performing 1 analyses: 0: [cluster crdset MYTRAJ :1-291@CA,N,C,O mass clusters 10 out cluster_out nofit averagelinkage summary summary_out info Cluster_info repout box2.rep repfmt pdb clusterout cluster.nc clusterfmt netcdf] Starting clustering. TIME: Analyses took 0.2995 seconds. DATASETS: 2 data sets: MYTRAJ "MYTRAJ" (trajectories), size is 250000 (1 trajectories) Cnum_00001 "Cnum_00001" (integer), size is 0 DATAFILES: cluster_out (Standard Data File): Cnum_00001 Warning: Set 'Cnum_00001' contains no data. Warning: File 'cluster_out' has no sets containing data. ---------- RUN END --------------------------------------------------- TIME: Total execution time: 648.5006 seconds.