[AMBER] How to obtain an ideal helix structure of Alanine 5 peptide (ACE-Ala5-NME) ?

From: Dongshan Wei <dswei0523.gmail.com>
Date: Thu, 18 Mar 2010 17:28:54 -0400

Hi All,

I need to calculate the RMSD of Ala5 (ACE-Ala5-NME) peptide in water and
want to choose an ideal alpha-helix structure as my reference structure.
Does anyone know how or where to obtain the ideal alpha-helix structure of
peptides? I looked through the PDB data bank and there is no such a short
peptide crystal structure.

Thanks!

Dongshan
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Received on Thu Mar 18 2010 - 14:30:03 PDT