Hi,
I am using cpptraj to cluster a trajectory. My input file looks like this:
(...)
trajin ../../../../prod03_025.mdcrd 1
strip :WAT
strip :Na+
strip :Cl-
cluster C1 hieragglo clusters 3 averagelinkage rms mass out
clusters_003.agr gracecolor summary clusters_003.sum info
clusters_003.info repout clusters_003 repfmt pdb
Though the procedure goes to the end and produces the requested number
of clusters, I have noticed that the output includes two warnings:
> [cluster C1 hieragglo clusters 3 averagelinkage rms mass out clusters_003.agr gracecolor summary clusters_003.sum info
> clusters_003.info repout clusters_003 repfmt pdb]
> CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (all atoms), mass-weighted best fit Hierarchical Agglomerative: 3 clusters, average-linkage.
> Cluster # vs time will be written to clusters_003.agr
> Grace color instead of cluster number (1-15) will be saved.
> Cluster information will be written to clusters_003.info
> Summary of cluster results will be written to clusters_003.sum
> Cluster representatives will be written to separate trajectories,
> prefix (clusters_003), format PDB
> Warning: [cluster] Not all arguments handled: [ rms ]
> Warning: One or more analyses requested creation of default COORDS DataSet.
> CREATECRD: Saving coordinates from Top u1e2h2_1_exdR_sol.prmtop to "_DEFAULTCRD_"
>
The second one is expected, but what does the first one mean? In this
example I didn't provide a mask (probably not very sensible) but if I
give a mask after the 'rms' option (like 'rms :
59-68.CA mass') I get:
> [cluster C1 hieragglo clusters 3 averagelinkage rms :59-68.CA mass out clusters_003.agr gracecolor summary clusters_003.sum info clusters_003.info repout clusters_003 repfmt pdb]
> CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:59-68.CA]), mass-weighted best fit
> Hierarchical Agglomerative: 3 clusters, average-linkage.
> Cluster # vs time will be written to clusters_003.agr
> Grace color instead of cluster number (1-15) will be saved.
> Cluster information will be written to clusters_003.info
> Summary of cluster results will be written to clusters_003.sum
> Cluster representatives will be written to separate trajectories,
> prefix (clusters_003), format PDB
> Warning: [cluster] Not all arguments handled: [ rms ]
> Warning: One or more analyses requested creation of default COORDS DataSet.
> CREATECRD: Saving coordinates from Top u1e2h2_1_exdR_sol.prmtop to "_DEFAULTCRD_"
>
So it looks that the mask and hence 'rms' is actually handled. Or is it not?
Cheers,
--
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombardia.afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
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Received on Mon May 13 2013 - 08:30:02 PDT
