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
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:55 CST