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

From: M. L. Dodson <>
Date: Thu, 18 Mar 2010 19:49:14 -0500

On Thu, Mar 18, 2010 at 05:36:06PM -0400, Adrian Roitberg wrote:
> 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

In the ambertools distribution, one of the nab example programs,
peptide, can be used to build oligopeptides of a single secondary
structure. At one time, the available structure data base for peptide
was patched to include the parameters for polyproline II. An
ambertools distribution is not readily available to me right now, but
it should be easy to check. You will have to compile the nab program.

Bud Dodson
M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
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Received on Thu Mar 18 2010 - 18:00:03 PDT
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