Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial

From: Thomas Cheatham III <>
Date: Fri, 4 Dec 2009 10:01:35 -0700 (Mountain Standard Time)

> trajin fzd2_w_md5.mdcrd
> cluster out avg-1 representative none average none all none averagelinkage clusters 1 mass rms
> "(:1-240) & .CA,C,N,O"
> go

The "none" keyword means you are choosing not to dump any coordinate
output for the "representative" snapshot (that closest to the centroid),
the "average" over each cluster, and dumping of "all" the frames in each

Also, I do not not understand why you would want to cluster into a single
(cluster 1) cluster as this will simply give back your original

cluster out c-out representative pdb average pdb averagelinkage \
  clusters 10 mass rms :1-240.CA,C,N,O

will create

c-out.avg.n <- average structures for each cluster as PDB
c-out.rep.n <- representative " "
c-out.n <- trajectories in mdcrd format for each cluster

-- tec3

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Received on Fri Dec 04 2009 - 09:30:02 PST
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