From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Jan 29 2013 - 08:27:01 CST
See STRIDE, a tool that does the secondary structure computation in VMD. You
should be able to use it to do what you want, but not without little
scripting effort.
Norman Geist.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Aditya Ranganathan
Gesendet: Dienstag, 29. Januar 2013 11:15
An: Norman Geist
Cc: Namd Mailing List
Betreff: Re: namd-l: Percentage of Residues in Ramachandran Plot regions
versus time of trajectory
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.
Regards
Srivastav Ranganthan
On Mon, Jan 28, 2013 at 11:38 AM, Norman Geist
<norman.geist_at_uni-greifswald.de> 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: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Aditya Ranganathan
Gesendet: Montag, 28. Januar 2013 05:45
An: vmd-l_at_ks.uiuc.edu; 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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