Going on first principles with no knowledge of cpptraj, did you define
any output files in your .in file?
Bill
On 9/25/17 2:22 AM, Sowmya Indrakumar wrote:
> Dear All,
> I am doing cluster analysis using the following script from: http://www.amber.utah.edu/AMBER-workshop/London-2015/Cluster/
>
>
> I get this message after it's complete with no output file. I even changed the cutoff of minpoints and epsilon, it still gives the same message.
>
> cpptraj ../../model_sol.mod.parm7 cpptraj.in
>
> CPPTRAJ: Trajectory Analysis. V17.00
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | Date/time: 09/25/17 10:55:25
> | Available memory: 3.626 GB
>
> Reading '../../model_sol.mod.parm7' as Amber Topology
> Radius Set: H(N)-modified Bondi radii (mbondi2)
> INPUT: Reading input from 'cpptraj.in'
> [trajin ../../5.0/prod_pH.nc]
> Reading '../../5.0/prod_pH.nc' as Amber NetCDF
> [strip :Na+ outprefix noions]
> STRIP: Stripping atoms in mask [:Na+]
> Stripped topology will be output with prefix 'noions'
> [cluster C0 dbscan minpoints 25 epsilon 0.9 sievetoframe rms :1-677.CA,N,C sieve 100 out cnumvtime.dat summary summary.dat info info.dat cpopvtime cpopvtime.agr normframe repout rep repfmt pdb singlerepout singlerep.nc singlerepfmt netcdf avgout Avg avgfmt restart]
> CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:1-677.CA,N,C]) best-fit
> DBSCAN:
> Minimum pts to form cluster= 25
> Cluster distance criterion= 0.900
> Sieved frames will only be added back if they are within
> 0.900 of a frame in an existing cluster.
> (This option is more accurate and will identify sieved
> frames as noise but is slower.)
> Initial clustering sieve value is 100 frames.
> Only non-sieved frames will be used to calc within-cluster average.
> Cluster # vs time will be written to cnumvtime.dat
> Cluster pop vs time will be written to cpopvtime.agr (normalized by frame)
> Pairwise distance data set is 'C0[PWD]'
> Cluster information will be written to info.dat
> Summary of cluster results will be written to summary.dat
> Representative frames will be chosen by closest distance to cluster centroid.
> Cluster representatives will be written to 1 traj (singlerep.nc), format Amber NetCDF
> Cluster representatives will be written to separate trajectories,
> prefix (rep), format PDB
> Average structures for clusters will be written to Avg, format Amber Restart
> Warning: One or more analyses requested creation of default COORDS DataSet.
> CREATECRD: Saving coordinates from Top model_sol.mod.parm7 to "_DEFAULTCRD_"
> ---------- RUN BEGIN -------------------------------------------------
>
> PARAMETER FILES (1 total):
> 0: model_sol.mod.parm7, 82378 atoms, 24759 res, box: Orthogonal, 24083 mol, 23978 solvent
>
> INPUT TRAJECTORIES (1 total):
> 0: 'prod_pH.nc' is a NetCDF AMBER trajectory, Parm model_sol.mod.parm7 (Orthogonal box) (reading 20000 of 20000)
> Coordinate processing will occur on 20000 frames.
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM 'model_sol.mod.parm7' (2 actions):
> 0: [strip :Na+ outprefix noions]
> Stripping 45 atoms.
> Stripped topology: 82333 atoms, 24714 res, box: Orthogonal, 24038 mol, 23978 solvent
> Writing topology 0 (model_sol.mod.parm7) to 'noions.model_sol.mod.parm7' with format Amber Topology
> 1: [createcrd _DEFAULTCRD_]
> Warning: COORDS data sets do not store times.
> Estimated memory usage (20000 frames): 19.760 GB
> ----- prod_pH.nc (1-20000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> Read 20000 frames and processed 20000 frames.
> TIME: Avg. throughput= 46.0936 frames / second.
>
> ACTION OUTPUT:
>
> ANALYSIS: Performing 1 analyses:
> 0: [cluster C0 dbscan minpoints 25 epsilon 0.9 sievetoframe rms :1-677.CA,N,C sieve 100 out cnumvtime.dat summary summary.dat info info.dat cpopvtime cpopvtime.agr normframe repout rep repfmt pdb singlerepout singlerep.nc singlerepfmt netcdf avgout Avg avgfmt restart]
> Starting clustering.
> Mask [:1-677.CA,N,C] corresponds to 2031 atoms.
> Estimated pair-wise matrix memory usage: > 79.664 kB
> Pair-wise matrix set up with sieve, 20000 frames, 200 sieved frames.
> Calculating pair-wise distances.
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete.
> Memory used by pair-wise matrix and other cluster data: 160.512 kB
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> No clusters found.
> Cluster timing data:
> TIME: Cluster Init. : 0.0011 s ( 0.01%)
> TIME: Pairwise Calc.: 7.5530 s ( 73.76%)
> TIME: Clustering : 0.0010 s ( 0.01%)
> TIME: Cluster Post. : 0.0000 s ( 0.00%)
> TIME: Cluster renumbering/sieve restore 0.0000 s ( 0.00%)
> TIME: Find best rep. 0.0000 s ( 0.00%)
> TIME: Info calc 0.0000 s ( 0.00%)
> TIME: Summary calc 0.0000 s ( 0.00%)
> TIME: Coordinate writes 0.0000 s ( 0.00%)
> TIME: Total: 10.2406 s
>
> TIME: Analyses took 10.2480 seconds.
>
> DATASETS (3 total):
> _DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 20000 (19.760 GB) Box Coords, 82333 atoms
> C0 "C0" (integer), size is 0
> C0[PWD] "C0[PWD]" (cluster matrix), size is 19900
>
> DATAFILES (2 total):
> cnumvtime.dat (Standard Data File): C0
> cpopvtime.agr (Grace File):
> Warning: Set 'C0' contains no data.
> Warning: File 'cnumvtime.dat' has no sets containing data.
> Warning: File 'cpopvtime.agr' has no sets containing data.
>
> RUN TIMING:
> TIME: Init : 0.0000 s ( 0.00%)
> TIME: Trajectory Process : 433.8995 s ( 94.95%)
> TIME: Action Post : 0.0424 s ( 0.01%)
> TIME: Analysis : 10.2480 s ( 2.24%)
> TIME: Data File Write : 0.0012 s ( 0.00%)
> TIME: Other : 12.7649 s ( 0.03%)
> TIME: Run Total 456.9560 s
> ---------- RUN END ---------------------------------------------------
> TIME: Total execution time: 457.5483 seconds.
> --------------------------------------------------------------------------------
> To cite CPPTRAJ use:
> Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
> Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
> Theory Comput., 2013, 9 (7), pp 3084-3095.
>
>
> Kindly, suggest what I'm doing wrong.
>
> Thanks
> Regards
> Sowmya
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Received on Mon Sep 25 2017 - 02:30:03 PDT
