[gmx-users] gmx do_dssp

[John Whittaker]

> but I don't know what those letters (E, S H etc) means.

I haven't used DSSP analysis in GROMACS but I have in AMBER, so I assume
the letters indicate the type of secondary structure for each residue as
given below:

"The output of DSSP is explained extensively under 'explanation'. The very
short summary of the output is:

    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

A blank in the DSSP secondary structure determination stands for loop or
irregular. Loops and irregular elements are often, very incorrectly,
called "random coil" or "coil". Many programs, including the PDBFINDER,
replace this blank by a C (doing undue justice to the historical
artefactual naming of loops and irregular stretches) because one never
knows if a blank means loop or no-output, or something-went-wrong."

I took this ^ straight from the DSSP webpage at
https://swift.cmbi.umcn.nl/gv/dssp/ under the "Output Short" section. Read
the DSSP manual, too, as suggested in the GROMACS manual in section 8.14.