[AMBER] clustering

From: Sowmya Indrakumar <soemya.kemi.dtu.dk>
Date: Tue, 31 Jan 2017 15:03:32 +0000

Dear All,
I am trying to get different representative structures from the trajectory file using this as an input (see below) using cpptraj:

parm *.parm7
trajin *.mdcrd
test clusters 5 rms .CA repout cluster repfmt pdb averagelinkage

running the above commands gives me 5 representative structures. It is not very clear to me what is it taking as the reference structure. Comparing the five generated representative pdb structure to the average pdb (from the trajectory) does not give show any trend in RMSD.

Kindly, let me know. if this is the right way to generate few presentative structures.

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Received on Tue Jan 31 2017 - 07:30:02 PST
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