# DSSP wont run for one chain of dimeric peptide connected by dissulfide bond
**URL:** https://gromacs.bioexcel.eu/t/dssp-wont-run-for-one-chain-of-dimeric-peptide-connected-by-dissulfide-bond/9234
**Category:** User discussions
**Tags:** analysis-tools
**Created:** [May 27, 2024, 1:46pm UTC](https://gromacs.bioexcel.eu/t/dssp-wont-run-for-one-chain-of-dimeric-peptide-connected-by-dissulfide-bond/9234 "2024-05-27T13:46:18Z")
**Posts on this page:** 7
**Page:** 1
### Author:  [@TGaziri](https://gromacs.bioexcel.eu/u/TGaziri)
#### Post date: [May 27, 2024, 1:46pm UTC](https://gromacs.bioexcel.eu/t/dssp-wont-run-for-one-chain-of-dimeric-peptide-connected-by-dissulfide-bond/9234/1 "2024-05-27T13:46:18Z")
GROMACS version: 2022
GROMACS modification: No
I’m trying to run `gmx do_dssp` on a dimeric peptide in which the chains are connected by a dissulfide bond. When generating the topology with pdb2gmx I merged both chains into a single molecule.
But when I try to run `gmx do_dssp` it simply goes into an infinity loop and never stops. So I tried indexing each chain separately. It worked for one chain but not for the other.
I know it probably has something to do with the dissulfide bond, but it doesn’t make any sense.
Odly enough `gmx dssp` from Gromacs 2023, works for it, but it won’t generate the dssp plot that really I need.
I’m 100% certain that my dssp is setup correctly, it works for literally everything else. I’ve checked multiple times.
Thanks
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### Author:  [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)
#### Post date: [May 28, 2024, 7:53am UTC](https://gromacs.bioexcel.eu/t/dssp-wont-run-for-one-chain-of-dimeric-peptide-connected-by-dissulfide-bond/9234/2 "2024-05-28T07:53:16Z")
Does `gmx dssp` in GROMACS 2024 work for you? Otherwise, what plot types are you missing?
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### Author:  [@TGaziri](https://gromacs.bioexcel.eu/u/TGaziri)
#### Post date: [May 28, 2024, 8:36pm UTC](https://gromacs.bioexcel.eu/t/dssp-wont-run-for-one-chain-of-dimeric-peptide-connected-by-dissulfide-bond/9234/4 "2024-05-28T20:36:43Z")
Hi, Thank you for your reply.
I’m missing the following plot type:
I really need this plot because it’s how we have always performed secondary structure analysis in our group. It seems `gmx dssp` is incapable of producing such a plot.
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### Author:  [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)
#### Post date: [May 29, 2024, 5:11am UTC](https://gromacs.bioexcel.eu/t/dssp-wont-run-for-one-chain-of-dimeric-peptide-connected-by-dissulfide-bond/9234/5 "2024-05-29T05:11:59Z")
Does this thread (not the first posts) help [How to read the dssp.dat file gmx 2023.1](https://gromacs.bioexcel.eu/t/how-to-read-the-dssp-dat-file-gmx-2023-1/9063)?
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### Author:  [@TGaziri](https://gromacs.bioexcel.eu/u/TGaziri)
#### Post date: [May 29, 2024, 9:46pm UTC](https://gromacs.bioexcel.eu/t/dssp-wont-run-for-one-chain-of-dimeric-peptide-connected-by-dissulfide-bond/9234/6 "2024-05-29T21:46:47Z")
Hi, thank you for your reply, unfortunately this thread doesn’t help me. I really need the dssp graph in which the secondary structures are represented by colors and we have the residue numbers on the y axis (like I previously showed). It is generated as a xpm file which you can convert to a eps file using `gmx xpm2ps`.
I really need to find a work around to make `gmx do_dssp` work for both chains.
I know it might be a problem only I have, but I really need the old `gmx do_dssp` functionality. I’d really appreciate if it was added to `gmx dssp` in the future.
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### Author:  [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)
#### Post date: [May 30, 2024, 1:52pm UTC](https://gromacs.bioexcel.eu/t/dssp-wont-run-for-one-chain-of-dimeric-peptide-connected-by-dissulfide-bond/9234/7 "2024-05-30T13:52:48Z")
I understand. Could you, please, submit a new feature request issue at [Issues · GROMACS / GROMACS · GitLab](https://gitlab.com/gromacs/gromacs/-/issues)?
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### Author:  [@TGaziri](https://gromacs.bioexcel.eu/u/TGaziri)
#### Post date: [June 4, 2024, 1:20pm UTC](https://gromacs.bioexcel.eu/t/dssp-wont-run-for-one-chain-of-dimeric-peptide-connected-by-dissulfide-bond/9234/8 "2024-06-04T13:20:28Z")
Sure, thanks