It is likely that the values for minpoints and epsilon are not
suitable for your system.
The tutorials are merely guidelines; examples of how you might go
about performing a certain kind of analysis. They are not designed to
be "plug and play" modules. If you are using a script you didn't
write, the best practice is to ensure you understand what each command
is doing. This way you can determine if the input is applicable to
your system or if it needs to be adjusted, or even removed. The manual
is an invaluable reference for this. For example, there is a section
in the Amber17 manual that specifically discusses choosing parameters
for DBSCAN clustering (page 656). As Tom said, clustering is more of
an art than a science and you'll probably need to play around with the
input parameters a bit.
Hope this helps,
-Dan
On Mon, Sep 25, 2017 at 5:22 AM, Sowmya Indrakumar <soemya.kemi.dtu.dk> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 25 2017 - 06:00:06 PDT
