AMBER Archive (2007)

Subject: AMBER: Is this system too large?

From: Hu, Shaowen \(JSC-SK\)[USRA] (Shaowen.Hu-1_at_nasa.gov)
Date: Tue Feb 20 2007 - 22:17:41 CST

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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