Hello.
I see the generated dat file from the gmx dssp command contains symbols not in the official DSSP site which contains the following:
H = α-helix
B = residue in isolated β-bridge
E = extended strand, participates in β ladder
G = 3-helix (310 helix)
I = 5 helix (π-helix)
T = hydrogen bonded turn
S = bend
The output I’m gettin are: [‘=’, ‘P’, ‘S’, ‘~’]
I found somewhere that P means polyproline bends and the “~” (tilde) means no structure.
What is the “=” sign?
Also, is there a way to make an esp file out of the dat file generated by the gmx dssp command? Or do I have to revert back to the old 2019 GROMACS version?
Oh, I forgot to mention. My peptides don’t contain prolines, yet the DSSP output gives me the P symbol, which, according to a user on this forum, means a polyproline bend.
Hello. Sorry for the delay, I’m usually not visiting this forum.
“P” means κ-helix (aka poly-proline II helix), “=” means break (distance between peptide bond atoms > 2.5 Å), “S” means bend (chain curvature at the central residue i of five residues as the angle between the backbone direction of the first three and the last three residues) and “~” means loop (aka no special secondary structure designation).
New gmx dssp version does not generate X PixMap compatible matrix file as I never intended to do so.