# Gmx dssp gives wrong secondary structure results

**URL:** <https://gromacs.bioexcel.eu/t/gmx-dssp-gives-wrong-secondary-structure-results/8559>\
**Category:** User discussions\
**Created:** [March 9, 2024, 2:47am UTC](https://gromacs.bioexcel.eu/t/gmx-dssp-gives-wrong-secondary-structure-results/8559 "2024-03-09T02:47:12Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![THFKevin](https://avatars.discourse-cdn.com/v4/letter/t/96bed5/32.png) [@THFKevin](https://gromacs.bioexcel.eu/u/THFKevin)\
**Post date:** [March 9, 2024, 2:47am UTC](https://gromacs.bioexcel.eu/t/gmx-dssp-gives-wrong-secondary-structure-results/8559/1 "2024-03-09T02:47:12Z")

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GROMACS version: 2024.1  
GROMACS modification: No

Hi everyone,

I’m using the current GROMACS version that contained a new “dssp” command and removed the old “do\_dssp”. However, when I was trying to use the following command:

gmx dssp -s md\_start.pdb -f md\_aligned.xtc -o …/analysis/dssp.dat -num …/analysis/dssp\_num.xvg

the command only gives a “.dat” output file containing “~”, “S”, and “P”, which is entirely unphysical because my protein obviously contained alpha helices and beta sheets (with VMD).

For example, MDTraj gives this assignment:

` ~~~~~HHHHHHHHHTT~~~ SS ~~HHHHHHHHHHHHHHTT~B~SSS~SEEE~TTSHHHHHHT~SEEETT~HHHHHHHHHHHS~~~ HHHHHHHHHHS ~~~~ `

while gmx dssp gives this:

` ~~~~~SSSSSSSSSS~~~~ SS ~~SSSSSSSSSSSSSSS~~ S~SSS~S ~~~~SSSSSSSSSS~S~~~ SS ~~SSSSSSSSSSS~~ = ~~SSSSSSSSSSPP~~ `

This mismatch is so incomprehensible… Am I calling the gmx dssp the wrong way? Or is it a problem with gmx dssp?

Thank you all.

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**Author:** ![al42and](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/al42and/32/1393_2.png) [@al42and](https://gromacs.bioexcel.eu/u/al42and)\
**Post date:** [March 11, 2024, 11:32am UTC](https://gromacs.bioexcel.eu/t/gmx-dssp-gives-wrong-secondary-structure-results/8559/2 "2024-03-11T11:32:44Z")

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Hi,

Minor mismatches between different tools are expected, but what you describe does not look reasonable.

Would you mind sharing the input files? Ideally, check if the problem can be reproduced with a single frame instead of the full trajectory.

Pinging @alexxy.

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**Author:** ![alexxy](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alexxy/32/597_2.png) [@alexxy](https://gromacs.bioexcel.eu/u/alexxy)\
**Post date:** [March 11, 2024, 11:50am UTC](https://gromacs.bioexcel.eu/t/gmx-dssp-gives-wrong-secondary-structure-results/8559/3 "2024-03-11T11:50:51Z")

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Hi,

We did tests with some set of randomly selected proteins from pdb, and checked that output of gmx dssp and original DSSPv4 was the same. So I agreed with @al42and that to check if its issue with gmx dssp we need example/test files which have differences in assignment of secondary structures between two tools.

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**Author:** ![THFKevin](https://avatars.discourse-cdn.com/v4/letter/t/96bed5/32.png) [@THFKevin](https://gromacs.bioexcel.eu/u/THFKevin)\
**Post date:** [March 11, 2024, 3:06pm UTC](https://gromacs.bioexcel.eu/t/gmx-dssp-gives-wrong-secondary-structure-results/8559/4 "2024-03-11T15:06:03Z")

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Hello,

Thanks for your comments. I cannot disclose the pdb and the trajectory files in my original post, but I have another input pdb and the xtc trajectory available in this link that has the same problem: [gmx\_test\_dssp.zip - Google Drive](https://drive.google.com/file/d/1nU4_Udm2B6PuhamZfJilCPmN_gH22de_/view?usp=share_link)

And the gmx dssp result for one single frame (for the pdb only, with no trajectory input) was:

` ~~~S~~ SSSSS~SSSSSSSSSSSSSS~SSS ~~~~~~~~SS~~ SS ~~~S~~~~~~~ SS ~~SSSSSSSSSSSS~~~ SSS ~~~~~SSSS~~~~ SS ~~SSSSSSSS~~ SSS ~~~~~~~SS~~~ S ~~~~~ `

which was totally unreasonable (when compared with VMD visualization).

Please feel free to check out. Thank you very much.

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**Author:** ![Sorcerer](https://avatars.discourse-cdn.com/v4/letter/s/58956e/32.png) [@Sorcerer](https://gromacs.bioexcel.eu/u/Sorcerer)\
**Post date:** [March 11, 2024, 6:53pm UTC](https://gromacs.bioexcel.eu/t/gmx-dssp-gives-wrong-secondary-structure-results/8559/5 "2024-03-11T18:53:19Z")

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You’ll have to use `--hmode dssp --clear` options if you’re going to use .pdb extension(s) as input. Otherwise, hydrogen atoms will not be recognized.

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**Author:** ![KosarRahimi](https://avatars.discourse-cdn.com/v4/letter/k/b5a626/32.png) [@KosarRahimi](https://gromacs.bioexcel.eu/u/KosarRahimi)\
**Post date:** [January 10, 2025, 12:39am UTC](https://gromacs.bioexcel.eu/t/gmx-dssp-gives-wrong-secondary-structure-results/8559/6 "2025-01-10T00:39:20Z")

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Hello,  
I am using gmx2023 “dssp” for secondary structures. It cannot recognize beta sheet though. Although gmx2021 do\_dssp recognize some beta sheet structures and also VMD shows beta sheets for the same trajectory. Has anyone had same issues?

Thank you.

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**Author:** ![vvlad\_andr](https://avatars.discourse-cdn.com/v4/letter/v/eb9ed0/32.png) [@vvlad\_andr](https://gromacs.bioexcel.eu/u/vvlad_andr)\
**Post date:** [September 7, 2026, 2:49pm UTC](https://gromacs.bioexcel.eu/t/gmx-dssp-gives-wrong-secondary-structure-results/8559/7 "2026-09-07T14:49:14Z")

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Hello! I analyzed protein mCherry today and this program couldn’t detect all the beta-barrels.