[AMBER] RMSD-based clustering in CPPTRAJ/PTRAJ

From: anu chandra <anu80125.gmail.com>
Date: Fri, 20 Dec 2013 11:23:36 +0530

Dear Amber users,

I am doing a protein simulation with the protein size of 290 residues.
During the 50ns simulation, I have seen that two particular helices (
helix-1, residues 50-85 and helix-2, residues 265-280) fluctuate around 2-3
angstroms from its crystal structure position. Here I am trying to do a
RMSD-based clustering to get the most populated structures ( centroids)
with respect to the position of helix-1 and helix-2 along the 50ns
simulation. Below is the input I used to do the same in CPPTRAJ,

trajin ../11md.crd 1 2500 5
trajin ../12md.crd 1 2500 5
trajin ../13md.crd 1 2500 5
trajin ../14md.crd 1 2500 5
trajin ../15md.crd 1 2500 5
trajin ../16md.crd 1 2500 5

strip :WAT,:Na+

center :1-293 mass origin
image origin center

cluster :50-85,:265-280.CA,N,C,O mass clusters 10 out cluster_out
averagelinkage gracecolor summary summary_out info Cluster_info repout
centroid repfmt pdb


Unfortunately, when I align all the 10 cluster centroids I have seen that
the position of helix-1 and helix-2 are not changed much as they align
almost perfectly on top of the same from each of the centroid structure.

Am I doing anything wrong with the clustering script? Is there a way to
give RMSD cut-off while clustering?

Waiting for your valuable reply

Many thanks in advance

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Received on Thu Dec 19 2013 - 22:00:03 PST
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