AMBER Archive (2009)

Subject: Re: [AMBER] MMTSB cluster analysis versus ptraj cluster analysis

From: Thomas Cheatham III (
Date: Fri Oct 16 2009 - 10:33:22 CDT

> I have been working on a non-competitive enzyme reaction in explicit
> clusters.However, I can't seem to get the ptraj's cluster function
> working as it appears below:

> trajin enzyme.qmmm.traj
> cluster out reductase representative pdb average pdb means clusters 5 rms :1-84  

I will look into why it is core dumping, but you need to specify an
algorithm for the clustering.... There are many, each with different
characteristics and you will see that each creates different clusters for
MD trajectory data; see for example Shao et al., JCTC 3, 2312 (2007).

Here is what I use (the sieve is useful is you have lots of frames):

cluster out clusters/c20ns all amber representative pdb average pdb \
  averagelinkage sieve 10 clusters 10 rms :1-39


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