# DSSP Analysis with GROMACS
**URL:** https://gromacs.bioexcel.eu/t/dssp-analysis-with-gromacs/2880
**Category:** User discussions
**Created:** [September 28, 2021, 1:44pm UTC](https://gromacs.bioexcel.eu/t/dssp-analysis-with-gromacs/2880 "2021-09-28T13:44:27Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@Michaela](https://gromacs.bioexcel.eu/u/Michaela)
#### Post date: [September 28, 2021, 1:44pm UTC](https://gromacs.bioexcel.eu/t/dssp-analysis-with-gromacs/2880/1 "2021-09-28T13:44:27Z")
GROMACS version: 2019.6-amd
Hello,
I’d like to do dssp analysis with GROMACS do\_dssp. However when I do it, I always get the same weird pattern in my .dat file. It always looks like this (for all systems!):
10
~=~=~=~=~=~=~=~=~=~
~=~=~=~=~=~=~=~=~=~
~=~=~=~=~=~=~=~=~=~
~=~=~=~=~=~=~=~=~=~
~=~=~=~=~=~=~=~=~=~
~=~=~=~=~=~=~=~=~=~
…
I can’t figure out what can be the cause. My code seems to be OK:
gmx do\_dssp -f trajectory.xtc -s structure.pdb -n index.ndx -ssdump file.dat -dt 1000
My index file specifies 10 amino acids for which I want to use the DSSP analysis.
I use this version of dssp: dssp-2.0.4-linux-amd64
Have someone ever experienced this type of error and could give me an advice, please? Thank You
---
### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [September 29, 2021, 2:29am UTC](https://gromacs.bioexcel.eu/t/dssp-analysis-with-gromacs/2880/2 "2021-09-29T02:29:51Z")
I’m not familiar with the format of this data file, but ~ means coil and = indicates a chain separator.