Re: AMBER: Protein with maximum hydrogen bonds

From: Sanjeev B.S. <sanjeev.mbu.iisc.ernet.in>
Date: Sat, 27 Nov 2004 20:44:01 +0530 (IST)

> In my research project I need to do simulation on a protein with a lot
> of intramolecular hydrogen bonds (more the better). Does anyone know
> about a protein with maximum number of intramolecular hydrogen bonds in
> it; or is there any way by which I can get such a structure from PDB?

This is what I would do:

.. Download all the PDBs of proteins.
.. Write a script that:
  -> 'Protonates' (say using tleap/protonate) the protein atoms
  -> Finds all intra-molecular h-bonds (defining group SOLUTE in carnal)
  -> Count the number of such h-bonds.

>From the table of PDB-ID vs number of h-bonds, I'll pickup the protien of
interest.

The toughest part here is to d/l the PDBs, the rest is quite simple. And
also you need to know what is the kind of 'protein' you wish to (and can)
simulate (like single chain/multiple and total number of atoms). I
wouldn't attempt to pickup a viral-coat protein, a proteosome, a ribosome
or some structure with 5 angstrom resolution! So somewhere, probably
before the h-bond calculation, I'd check the size of the system to see if
I need to consider it at all!

Best wishes,
-Sanjeev
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Received on Sat Nov 27 2004 - 15:53:00 PST
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