In secondary structure analysis i just gave following command
parm 1L2Y_linear.prmtop
trajin trp_trj.nc
secstruct out dssp.dat
I need to do following analysis:
1. Calculate Secondary Structure Percentages To calculate the percentage
of time each residue spends in a structured element 2.Analyze Secondary
Structure Propensity / Per-Residue Stability
For each *residue*, I want to calculate what percentage of *time* it spent
in each state.
*How to read it:*
· A residue with *~100% *H is a very stable part of an alpha-helix.
· A residue with *~50% *H* and ~50% *C is in a dynamic region that
folds and unfolds during the simulation.
· I can identify which parts of a loop are flexible (C, T, S) and
which parts occasionally form stable elements like short β-strands (E).
I want to plot this propensity (e.g., % Helix vs. Residue Number) to create
a visual stability map of your protein.
In order to do so , i ran following python script..
But it gave me 0 % written in front of each residue...
I am attaching the python script .
can someone guide me where is the error or provide me the script to run
that?
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 04 2025 - 09:30:02 PDT
