AMBER Archive (2008)

Subject: AMBER: Cluster analysis

From: Francesco Pietra (
Date: Mon Jan 07 2008 - 10:00:40 CST

I am trying a cluster analysis with MMTSB, having as guideline tutorial A3.

Unlike that, once stripped the environment, I have two molecules, a protein and
its non-polymeric docked ligand. Is any general criterion to adapt to my case -
where the interest is in both molecules - tutorial's conditions for ptraj:

# orient all frames best fit to backbone in NMR structure
rms first mas :residueX-residueY_at_CA,C,N

taking into account that atom O (oxygen) is of utmost importance for the

Should the analysis be carried out separately for the protein and the ligand?

Hope the question is not to cryptic.

The first attempts were unsuccessful, though on simplex examples MMTSB did


francesco pietra

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