Hi Carlos
Thank you for the idea. I will definitely look at this paper.
Basically my aim of study is: I am trying to see the folding pattern of a
short peptide. It is going through an alpha helix. I would like to express
this helix formation in some way apart from just viewing the trajectory.
Thanks
Suchetana Gupta
Graduate Student
IIT Madras
On Tue, Apr 29, 2014 at 9:04 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> it depends on what you want to learn, and if you are comparing to
> experiment. If you look at CD, it's not a local measure of helix (not just
> phi/psi pair). In that case I would suggest using DSSP in cpptraj, or
> something like that. If you are comparing to NMR measures of helicity, such
> as those using chemical shift, then it is a more local conformation and you
> probably want phi/psi pairs.
>
> We have some examples of helicity measures in an older article from my lab
> Song, K., Stewart, J., Fesinmeyer, M. Andersen, N., Simmerling, C.,
> "Structural Insights for Designed Alanine-rich Helices: Comparing NMR
> Helicity Measures and Conformational Ensembles from Molecular Dynamics
> Simulation", Biopolymers, 89:747-760 (2008)
>
>
> On Tue, Apr 29, 2014 at 11:06 AM, Suchetana Gupta <
> suchetana.gupta.gmail.com
> > wrote:
>
> > Dear AMBER users
> > I have simulated a small peptide. It has a single alpha helix
> structure,a s
> > visible from the VMD view. I would like to quantify the helix formation.
> I
> > was thinking of looking at the dihedral angle between certain residues in
> > the helix over the entire trajectory to get some idea. Is this correct?
> Can
> > you suggest any other method to quantify the formation/time evolution of
> > the helix?
> > Thanks in advance for your help
> > Suchetana Gupta
> > Graduate Student
> > Department of Biotechnology
> > IIT Madras
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 29 2014 - 11:30:02 PDT
