Subject: Large biomolecules

From: "Victor Anisimov" <[email-masked]>
Date: Mon, 26 Nov 2001 12:40:48 +0100

Dear CCLers:

I'm looking for biggest available bio-molecule, preferably protein, for running
NDDO type quantum-chemical calculation on it on my Windows PC. 
Could someone please share with me Cartesian coordinates of such 
sample.

Before asking your help I investigated PDB database and could find only 
Chaperonin with PDB id 1AON containing about 120 000 atoms after 
adding hydrogen atoms. This molecule is not that big as I need. 

It may happen that there is no bigger experimentally available protein structure 
than the mentioned above. In this case I would be quite happy to get 
Cartesian coordinates of 3D structure of a really large protein created by 
some modeling program.

I also wonder is there any application that could read sequence of
DNA base letters and construct corresponding 3D model of the DNA? 
May I ask users of such program to generate a realistic 3D model of a Human
DNA fragment for me corresponding to single Gene (your favorite, for
example), that should produce several million atoms' structure, I believe.

Thank you for your time.

With kind regards,
Victor.

Victor Anisimov, PhD.
E-Mail: [email-masked]
Mobile: +48 606 945 326

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From: Andrey Khavryuchenko <[email-masked]>
Date: 26 Nov 2001 17:09:54 +0200

Victor,

"VA" == Victor Anisimov wrote:

 VA> I'm looking for biggest available bio-molecule, preferably protein,
 VA> for running NDDO type quantum-chemical calculation on it on my Windows
 VA> PC.  Could someone please share with me Cartesian coordinates of such
 VA> sample.

 VA> Before asking your help I investigated PDB database and could find
 VA> only Chaperonin with PDB id 1AON containing about 120 000 atoms after
 VA> adding hydrogen atoms. This molecule is not that big as I need.

I am curious why you would want such large protein to be calculated using
NDDO?

And, of course, what hardware and software you're going to utilize?

-- 
Andrey V Khavryuchenko          http://www.kds.com.ua/
Offshore Software Development