AMBER Archive (2007)

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

From: Hu, Shaowen \(JSC-SK\)[USRA] (Shaowen.Hu-1_at_nasa.gov)
Date: Wed Feb 21 2007 - 11:02:21 CST

Thanks a lot. My computational resource will allow me to run thus far.
Could you refer any papers that have done with similar systems? How will
the MM/PBSA work for energy calculation?

Best,

Shaowen Hu

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Fenghui Fan
Sent: Tuesday, February 20, 2007 10:53 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: Is this system too large?

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]"
<Shaowen.Hu-1_at_nasa.gov> 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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