I guess there must be some typo or an extra \, just recheck all commands.
Moreover, the AMBER Manual mentions a method on how to select an epsilon
and minpts, you might want to check that once.
On Thursday, July 11, 2019, Lod King <lodking407.gmail.com> wrote:
> 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
> 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 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
> centroid.
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Best Regards
Elvis Martis
Mumbai.
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Received on Wed Jul 10 2019 - 20:30:02 PDT
