[AMBER] Query on Rmsd between clusters and population

From: Athena N <athena.nas01.gmail.com>
Date: Fri, 4 Jun 2021 22:30:06 +0530

Dear all,

I have been doing some clustering analysis of a protein. The clusters are
randomly distributed with 31% being the major cluster. I am using tje
following input line:
Parm prot.prmtop
Trajin md2.nc 1 last 5
Strip :1201-1350
Cluster hieragglo epsilon 3 clusters 10 averagelinkage rms :1-1200.C,N,CA
sieve 10 out clus.dat summary clustersummary.dat info clusterinfo.dat

On superimposing the major representative clusters of these (30-12-11...)in
pymol, the structures look almost identical. Yet the clister distribution
is so random. So I have 2 queries
1. Is it possible to get the rms between these clusters via cpptraj itself
rather than the superimposing? If yes, please suggest the action to be used
2. My trajectory is 300ns long with 150,000 frames. Is it possible to know
to which cluster ,(out of the 10 generated ones), the structures in each of
these frames belongs? I mean to identify if the frame 10000 belongs to
cluster 1 or 3 ?

Kindly advise.
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Received on Fri Jun 04 2021 - 10:30:02 PDT
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