[gmx-users] secondary structure analysis DSSP

[Angelina Malagodi]

Hello,

I'm trying to evaluate the secondary structure of a monomer through the
DSSP software. Combined with a Gromacs trajectory the output gives "
Structure, Coil, B-Sheet, B-Bridge, Bend, Turn, A-Helix, 3-helix". This
output is different from the standard DSSP program. I cannot find any
documentation to explain what the criteria is for each secondary structure
with Gromacs. Can you please point me in the right direction?

Thank you so much,

Angelina Malagodi


Example output file:

#   gmx do_dssp -f 200ns_2lmnmon3.xtc -s md_1_54a7_2lmn_mon_3.tpr -tu ns
# gmx do_dssp is part of G R O M A C S:
#
# Giant Rising Ordinary Mutants for A Clerical Setup
#
@    title "Secondary Structure"
@    xaxis  label "Time (ns)"
@    yaxis  label "Number of Residues"
@TYPE xy
@ subtitle "Structure =  + B-Sheet + B-Bridge + Turn"
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Structure"
@ s1 legend "Coil"
@ s2 legend "B-Sheet"
@ s3 legend "B-Bridge"
@ s4 legend "Bend"
@ s5 legend "Turn"
@ s6 legend "5-Helix"
@ s7 legend "3-Helix"
       0     0    29     0     0     3     0     0     0
    0.01     2    29     0     0     1     2     0     0
    0.02     0    30     0     0     2     0     0     0
    0.03     2    30     0     0     0     2     0     0
    0.04     0    29     0     0     3     0     0     0
    0.05     2    27     0     0     3     2     0     0
    0.06     2    28     0     0     2     2     0     0
    0.07     0    28     0     0     4     0     0     0
    0.08     0    27     0     0     5     0     0     0
    0.09     0    27     0     0     5     0     0     0