Flexibility of protein secondary structures

User discussions
1

GROMACS version: 2019.4
GROMACS modification: No
Hi,
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,
Prithwish

2

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.

3

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