AMBER Archive (2007)

Subject: Re: AMBER: Is this system too large?

From: David A. Case (case_at_scripps.edu)
Date: Wed Feb 21 2007 - 18:05:39 CST

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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