AMBER Archive (2009)
Subject: Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial
From: Andrew Voronkov (drugdesign_at_yandex.ru)
Date: Sun Dec 06 2009 - 05:58:41 CST
Yes, larger motions have some influence as far as the binding site is in the interface of homodimer and there are some little oscillations in monomers distance. But I actually also want to optimize somehow the number of clusters.
04.12.09, 12:20, "Thomas Cheatham III" <tec3_at_utah.edu>:
> > 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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