[Biopython] clustering pdb

[Frederico Arnoldi]

Dear Bala,

As indicated by Rodrigues, you can use GromacsWrapper for peforming MD. I do not know any package for python that you could use to handle MD trajectories. However, it is possible to use RPy and Bio3D (http://mccammon.ucsd.edu/~bgrant/bio3d/index.html).

Att.,
Frederico Arnoldi

 
> Message: 1
> Date: Mon, 19 Jul 2010 11:39:11 +0200
> From: Bala subramanian 
> Subject: [Biopython] clustering pdb
> To: biopython at lists.open-bio.org
> Message-ID:
> 
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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.
>
> Is there any utility in Biopython to handle MD trajectories obtained from
> common packages like gromacs, amber etc ?
>
> Thank you,
> Bala
>
 		 	   		  
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