Flexibility of protein secondary structures

GROMACS version: 2019.4
GROMACS modification: No
I am working on protein-lipid bilayer and I am interested to calculate the flexibilities of various secondary structures, e.g. coils and one helix specifically.
Is there any gromacs tool or commands that can do this?
What would be a good metric to quantify the flexibility?
Thanks in advance,

Hi Prithwish,

you can try gmx do_dssp. Note that this a special gromacs tool in the sense that it calls itself a different tool that is not developed within GROMACS, mkdssp, which you will have to download and install separaterly, e.g., from https://github.com/cmbi/dssp .

A simple metric to analyse secondary structure assignment flexibility is the distance between the assigned secondary structure strings, below is a short python code fragment that does the job

def string_distance(a, b):
    distance = 0
    for charA, charB in zip(a,b):
        if (charA!=charB):
            distance += 1
    return distance

You might want to adapt the distance += 1 accordingly if you want to account for the fact that some secondary structure elements are more similar to another than others.

Hello, Thanks for your help. Let me explore this tool dssp and I’ll let you how it goes.
Thanks, Prithwish