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

From: Adrian Roitberg <roitberg.qtp.ufl.edu>
Date: Thu, 18 Mar 2010 17:36:06 -0400

To do what you want, you need to impose phi/psi ideal helical angles for
each alanine. You can do this by using the 'impose' command in leap.

However, and I cannot emphasize strongly enough: Ala_5 is NOT an alpha
helix !

It is a polyproline II structure, but highly flexible.

It is time people stop referring to alanine peptides as 'alpha helical'

Adrian


On 3/18/10 5:28 PM, Dongshan Wei wrote:
> 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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-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry
                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society
University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian.qtp.ufl.edu
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Received on Thu Mar 18 2010 - 15:00:02 PDT
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