Re: Percentage of Residues in Ramachandran Plot regions versus time of trajectory

From: Aditya Ranganathan (
Date: Tue Jan 29 2013 - 04:14:57 CST

Hello Norman,

I did try ptraj in the ambertools but it displays 0 for all fields. There
seems to be very little support on the ambertools mailing group regarding
the same. I was wondering if someone could englighten me on a vmd script
that just calculates the percentage of residues within the beta sheet
region of Ramachandrab plot and alpha helical region of Ramachandran Plot
versus time. In any case ptraj uses hbonding as a means for assigning
secondary structure. Please help me out on the same.


Srivastav Ranganthan*

On Mon, Jan 28, 2013 at 11:38 AM, Norman Geist <> wrote:

> You could be interested in ptraj, from the ambertools package. It has a
> option to read top/psf and dcd files and will output statistical
> information about the percentage of which residue being which secstruct.**
> **
> ** **
> Norman Geist.****
> ** **
> *Von:* [] *Im
> Auftrag von *Aditya Ranganathan
> *Gesendet:* Montag, 28. Januar 2013 05:45
> *An:*; NAMD list
> *Betreff:* namd-l: Percentage of Residues in Ramachandran Plot regions
> versus time of trajectory****
> ** **
> Hello All,
> I`m working in the area of protein aggregation and trying to use MD
> simulations to study the secondary structural progression during
> aggregation. However, I have a couple of questions. Is it possible to find
> out the percentage of residues falling in the alpha helical and beta sheet
> regions of the Ramachandran Plot versus time. Is there a script to do the
> same over the timeframe of the simulation. Also, would STRIDE secondary
> structural prediction results be drastically different from the
> Ramachandran plot residue assignment. I`m a novice at writing scripts. If
> there is an analysis script that does the same, it would be greatly
> appreciated.
> Thanks and Regards
> Srivastav Ranganathan
> Research Scholar
> IIT Bombay****

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