RE: AMBER: Is this system too large?

From: Hu, Shaowen \(JSC-SK\)[USRA] <"Hu,>
Date: Thu, 22 Feb 2007 09:58:01 -0600

Thanks a lot. I decided to switch to a smaller system, a subunit (51
residues) of this protein interacting with a 14-mer DNA. However, I do
not have an initial structure with both "molecules". Can I use Xleap to
prepare some starting points, in which the two "molecules" locate
themselves at specific position and distance?

Thanks for your kind guidance,

Shaowen Hu

-----Original Message-----
From: [] On Behalf
Of David A. Case
Sent: Wednesday, February 21, 2007 6:06 PM
Subject: Re: AMBER: Is this system too large?

On Tue, Feb 20, 2007, Hu, Shaowen (JSC-SK)[USRA] wrote:
> I am a novice to AMBER. After running some tutorials from your
> website, I tried my first project with AMBER 9. I am just wondering
> whether somebody can give me some ideas on the suitability of this
> system. If it is beyond the capability of AMBER, I may switch to other
smaller ones.
> The complex is composed of a protein heterodimer (1023 amino acids)
> and a 14-mer DNA. After added in oct water with least edge distance
> 8.0, it has
> 137451 total atoms. I am afraid that it may be too large to get
> reasonable comformational analysis and energetical analysis ( like the
MM/PBSA scheme).

Since you are a novice to Amber, I would recommend spending time to make
sure you understand how to run and analzye smaller systems (say
10-25,000 atoms) before embarking on a protein systems with over 1000
residues. If you survey the literature, I think you will find only a
few accounts of good simulations that are this big, and their authorship
is highly skewed to experienced investigators.

...good luck...dac
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Received on Sun Feb 25 2007 - 06:07:19 PST
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