From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Jan 28 2013 - 00:08:17 CST
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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