[AMBER] Cluster RMSD

From: Jenny 148 <jenny.rs140.gmail.com>
Date: Thu, 1 Jul 2021 11:05:37 +0530

Hi everyone,
I was clustering a set of protein trajectories using the following script.
parm prot.prmtop
trajin protein1_md.nc 1 last 5
cluster hieragglo epsilon 3 clusters 10 averagelinkage rms
sieve 10 out clusterout.dat summary clustersummary.dat info clusterinfo.dat
 repout rep repfmt pdb

 The clusters are very randomly distributed (the major cluster being just
30% in one of the system and around 17-20 in others). But when I
superimpose the representative structures of each of the system in PyMOL,
it seems like they are not very different from the major cluster. I would
like to know if
> it possible to obtain the exact RMSD between the 9 clusters with respect
to the first cluster out of the total 10 clusters generated?
> If we could specify an RMS value of the mask we are using according to
which the clustering is done?
Jenny R.S
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Received on Wed Jun 30 2021 - 23:00:03 PDT
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