Re: AMBER: Is this system too large?

From: Fenghui Fan <>
Date: Tue, 20 Feb 2007 20:53:26 -0800 (PST)

I think it can work. But you may have your productive
MD a little longer, for example 5 ns.

Best regards.

Fenghui Fan

--- "Hu, Shaowen (JSC-SK)[USRA]"
<> wrote:

> Dear All,
> 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).
> Thanks a lot,
> Shaowen Hu

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Received on Wed Feb 21 2007 - 06:07:49 PST
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