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 - 07:39:39 CST

PTRAJ CLUSTER: Clustering elapsed time: 38 seconds
  Printing distribution of distances to file c-out.txt
    Distribution of Distances
  [ 0.627, 0.805] -- 0.37% ( 456 out of 124750)
  [ 0.805, 0.984] -- 1.47% ( 1833 out of 124750)
  [ 0.984, 1.162] -- 3.83% ( 4776 out of 124750)
  [ 1.162, 1.341] -- 7.60% ( 9482 out of 124750)
  [ 1.341, 1.519] -- 12.56% ( 15668 out of 124750)
  [ 1.519, 1.698] -- 14.62% ( 18244 out of 124750)
  [ 1.698, 1.877] -- 13.53% ( 16877 out of 124750)
  [ 1.877, 2.055] -- 11.74% ( 14644 out of 124750)
  [ 2.055, 2.234] -- 10.02% ( 12497 out of 124750)
  [ 2.234, 2.412] -- 8.30% ( 10350 out of 124750)
  [ 2.412, 2.591] -- 6.25% ( 7791 out of 124750)
  [ 2.591, 2.769] -- 4.05% ( 5050 out of 124750)
  [ 2.769, 2.948] -- 2.41% ( 3001 out of 124750)
  [ 2.948, 3.126] -- 1.50% ( 1872 out of 124750)
  [ 3.126, 3.305] -- 0.94% ( 1177 out of 124750)
  [ 3.305, 3.483] -- 0.47% ( 584 out of 124750)
  [ 3.483, 3.662] -- 0.24% ( 303 out of 124750)
  [ 3.662, 3.841] -- 0.09% ( 114 out of 124750)
  [ 3.841, 4.019] -- 0.02% ( 27 out of 124750)
  [ 4.019, 4.198] -- 0.00% ( 4 out of 124750)

04.12.09, 12:20, "Thomas Cheatham III" :

>
> > 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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>
>

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