Thanks a lot to Adrian and Bud.
Another question, is there any published papers pointing out the folded
structure of Ala_5 is Polyproline II instead of alpha-helix?
Dongshan
On Thu, Mar 18, 2010 at 8:49 PM, M. L. Dodson <
activesitedynamics.comcast.net> wrote:
> 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
> Personal Email: mldodson-at-comcast-dot-net
> Phone: eight_three_two-56_three-386_one
>
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--
-----------------------------------------------------------------------------------
Dr. Dongshan Wei
Department of Chemistry
Boston University
Boston, MA, 02215
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Received on Fri Mar 19 2010 - 10:00:03 PDT
