The gromacs tool do_dssp (freeware) uses the dssp program for a graphical output. In it's -cs output (scount.xvg) it gives you the secondary structure in the following form:
@ s0 legend "Structure"
@ s1 legend "Coil"
@ s2 legend "B-Sheet"
@ s3 legend "B-Bridge"
@ s4 legend "Bend"
@ s5 legend "Turn"
@ s6 legend "A-Helix"
@ s7 legend "5-Helix"
@ s8 legend "3-Helix"
# SS % 0.67 0.17 0.13 0.01 0.11 0.16 0.38 0.00 0.05
Priyamvada P. ...... Priyamvada I added, "with gromacs tool do_dssp how to derive percentage from dssp.xvg" to a Google search and found a series of links that may be helpful. In particular an older ResearchGate comment and links to the gromacs user forums. You could send an internal ResearchGate message from the contributors profile page. And contact the user forums. The additional may help too.
I do not use this software. Just trying to offer help. Please let me know if you need help accessing the links I'm looking at.
Hi Priyamvada P.,
To calculate the percentage of a specific secondary structure, such as an α-helix, through counting the number of occurrences of that structure and dividing it by the total number of secondary structures created, you can follow these steps:
1. Open the file "scount.xvg" using a text editor such as Notepad++.
2. Look for the section that displays the secondary structures.
3. Count the number of occurrences of the specific structure you are interested in, such as α-helix.
4. Count the total number of secondary structures.
5. Divide the number of occurrences of the specific structure by the total number of secondary structures.
6. Multiply the result by 100 to obtain the percentage.
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