[AMBER] Cluster Analysis with CPPTRAJ

From: Lod King <lodking407.gmail.com>
Date: Wed, 10 Jul 2019 19:39:45 -0700

Hi Amber

I saw a workshop tutorial online for Clustering and tried to follow the
command :

*>parm abc.prmtop*

*>trajin abc.dcd*
*>cluster c0 \ dbscan minpoints 25 epsilon 0.9 sievetoframe \ rms :1-42.CA
\ sieve 2000 random \ out cnumvtime.dat \ sil Sil \ summary summary.dat \
info info.dat\ cpopvtime cpopvtime.agr normframe \ repout rep repfmt pdb \
singlerepout siglerrep.nc <http://siglerrep.nc> singlerepfmt netcdf \
avgout Avg avgfmt restart*

but got the following message:

    CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask
[:1-42.CA]) best-fit
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 will be randomly sieved (with value 2000).
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
Frame silhouettes will be written to Sil.frame.dat, cluster silhouettes
 will be written to Sil.cluster.dat
Silhouette calculation will use non-sieved frames ONLY.
Representative frames will be chosen by closest distance to cluster
Cluster representatives will be written to 1 traj (siglerrep.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
Error: [cluster] Not all arguments handled: [ \ \ \ \ \ \ \ \ \ \ ]

Did I miss anything?
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Received on Wed Jul 10 2019 - 20:00:02 PDT
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