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
