[Biopython] clustering pdb

[Peter]

On Mon, Jul 19, 2010 at 10:39 AM, Bala subramanian
<bala.biophysics at gmail.com> wrote:
> Friends,
> I have around 3000 pdb files obtained from MD simulations. I would like to
> know if it is possible to cluster the pdb files using any of the biopython's
> bio.PDB or other modules. If so, i would appreciate if you could provide me
> a sample code.

What kind of clustering do you want to do? By folds/structure? By sequence?

> Is there any utility in Biopython to handle MD trajectories obtained from
> common packages like gromacs, amber etc ?

No, we don't do any molecular dynamics - try The Molecular Modelling Toolkit
(MMTK) by Konran Hinsen for a Python MD toolkit:
http://dirac.cnrs-orleans.fr/MMTK/

Peter