Re: [AMBER] DBscan gives me errors in clustering

From: Daniel Roe <>
Date: Wed, 25 Mar 2020 15:18:53 -0400


The 'kdist' option is just for helping you choose minpoints and
epsilon, not actually performing the clustering. The error message
should be more informative here. So to summarize; if you're using
kdist to choose minpoints and epsilon, don't specify anything else


On Wed, Mar 11, 2020 at 11:40 AM Debarati DasGupta
<> wrote:
> Hi I am trying to cluster my trajectory for a simple protein in TIP3P water simulation
> My input for dbscan clustering is
> parm strip_2XXX.prmtop
> trajin 2XXX_stripped.mdcrd 1 last
> cluster D1 dbscan epsilon 2.0 kdist 3 kfile kdist_data sievetoframe rms :2-151.C,N,O,CA,CB&!.H= random out cnumvtime-dbscan.dat summary summary-dbscan.dat info info-dbscan.dat cpopvtime cpopvtime-dbscan.agr normframe repout rep-dbscan repfmt pdb singlerepout singlerep fmt netcdf avgout avg-dbscan avgfmt pdb
> run
> Any advice on how to troubleshoot this??
> Error I get is
> CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:2-151.C,N,O,CA,CB&!.H=]) best-fit
> Only calculating Kdist graph for K=3
> Kdist file prefix: kdist_data/
> Cluster # vs time will be written to cnumvtime-dbscan.dat
> Cluster pop vs time will be written to cpopvtime-dbscan.agr (normalized by frame)
> Pairwise distance data set is 'DB1[PWD]'
> Cluster information will be written to info-dbscan.dat
> Summary of cluster results will be written to summary-dbscan.dat
> Representative frames will be chosen by lowest cumulative distance to all other frames.
> Cluster representatives will be written to 1 traj (, format Amber NetCDF
> Cluster representatives will be written to separate trajectories,
> prefix (rep-dbscan), format PDB
> Average structures for clusters will be written to avg-dbscan, format PDB
> Error: [cluster] Not all arguments handled: [ minpoints 10 epsilon 2.0 sievetoframe ]
> 1 errors encountered reading input.
> Warning: Set 'DB1' contains no data.
> Warning: File 'cnumvtime-dbscan.dat' has no sets containing data.
> Warning: File 'cpopvtime-dbscan.agr' has no sets containing data.
> TIME: Total execution time: 0.1114 seconds.
> Error: Error(s) occurred during execution.
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Received on Wed Mar 25 2020 - 12:30:02 PDT
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