[AMBER] Clustering of MD trajectories: ptraj, cpptraj

From: Francesco Gentile <fgentile.ualberta.ca>
Date: Thu, 19 May 2016 12:41:16 -0600

I want to perform rmsd-based clustering of an MD trajectory. As I want to
find the optimal number of clusters based on the DBI and the SSR/SST ratio
as explained in Shao's 2007 paper, I was planning to use ptraj as it gives
as output these indexes. However I notice that it does automatically an
rmsd-fit to the specified mask on which the clustering is performed. this
is my script

"center :1-132 mass origin
image origin center familiar
rms first mass ':1-132.CA,C,N'
cluster out clustering representative pdb averagelinkage clusters 1 rms
mass ':6,8,9,33,34,44,45,46,50' nofit"

and the nofit does not work for this; my understanding is that with this
script the clustering will be anyway performed on a trajectory best-fitted
to the mask, and I am not sure this is the best way to account for
different conformations of these residues. Now, I can specify nofit in
cpptraj but it does not give the SSR/SST ratio in the output. I am looking
for a solution for either:

1) avoid the fitting during the clustering on the clustered residues


2) get the SSR/SST ratio from cpptraj

I can use both AmbertTools13 and 14. Any help will be greatly appreciated.

Francesco Gentile
PhD Student, Biophysics
CCIS 3-215, Department of Physics
7-112, Li Ka Shing Centre for Health Research Innovation
University of Alberta, Edmonton, AB T6G 2E1
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Received on Thu May 19 2016 - 12:00:04 PDT
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