AMBER Archive (2009)

Subject: Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial

From: Thomas Cheatham III (
Date: Fri Dec 04 2009 - 13:20:21 CST

> I actually want to divide trajectory of 5000 snapshots from 5
> nanoseconds into 10-20 representative structures as it is done in
> relaxed complex scheme, but in my case i dont have a ligand, just want
> to simulate the protein flexibility by usage of most common structures
> with rigid docking. So what procedure is best for such a purpose and is
> there anywhere more detailed description of these procedures?

What I would do, if trying to select structures for docking is come up
with a list of active site residues, and then cluster to these... Let's
assume the active site is residues 10,11,15,20.

cluster out reps20 representative pdb average none all none averagelinkage \
  clusters 20 mass rms :10,11,15,20

If you are concerned about larger motions of the entire protein use all
protein residues...

-- tec3

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