# Pdb2gmx does not recognize disulfides accurately

**URL:** <https://gromacs.bioexcel.eu/t/pdb2gmx-does-not-recognize-disulfides-accurately/5960>\
**Category:** User discussions\
**Tags:** pdb2gmx\
**Created:** [March 11, 2023, 4:28pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-does-not-recognize-disulfides-accurately/5960 "2023-03-11T16:28:20Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![arash7394](https://avatars.discourse-cdn.com/v4/letter/a/3da27b/32.png) [@arash7394](https://gromacs.bioexcel.eu/u/arash7394)\
**Post date:** [March 11, 2023, 4:28pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-does-not-recognize-disulfides-accurately/5960/1 "2023-03-11T16:28:20Z")

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GROMACS version: 2022.3  
GROMACS modification: No  
Dear GROMACS users,

I have a protein-protein complex with seven disulfide bonds and a free cysteine. However, pdb2gmx only recognizes four of the disulfides and leaves the other three as free cysteine. I know this is the case as the disulfides lack the HG atom and have the S-S bond parameterized under [bonds] in the topology file, whereas the free cysteines do not. Is there any way around this? Maybe by changing the name of Cys residues in the input pdb?

Thanks  
Arash Firouzbakht

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [March 15, 2023, 3:31pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-does-not-recognize-disulfides-accurately/5960/2 "2023-03-15T15:31:12Z")

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Hi,  
did you try to assign S-S manually by using the option -ss in gmx pdb2gmx ?  
Also if you have S-S bridge between different chains, you may need to use also the option -merge.  
I hope it helps  
Alessandra

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**Author:** ![arash7394](https://avatars.discourse-cdn.com/v4/letter/a/3da27b/32.png) [@arash7394](https://gromacs.bioexcel.eu/u/arash7394)\
**Post date:** [March 15, 2023, 5:56pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-does-not-recognize-disulfides-accurately/5960/3 "2023-03-15T17:56:51Z")

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Alessandra,

using -merge actually took care of one of missing disulfides! For the other ones, it says in the manual that the S-S distance needs to be within 10% of the specified bond length for S-S in specbond.dat (2Å ± 0.2Å). Since my structures are generated by AlphaFold, some of the disulfides were a bit shorter than the cutoff so pdb2gmx left them as free Cys. I am now trying to fix the bond lengths and relax the structure after that.

-Arash

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**Author:** ![H3nrasouli](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/h3nrasouli/32/1373_2.png) [@H3nrasouli](https://gromacs.bioexcel.eu/u/H3nrasouli)\
**Post date:** [January 5, 2024, 4:55pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-does-not-recognize-disulfides-accurately/5960/4 "2024-01-05T16:55:46Z")

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You can manually edit the specbond.dat file. You should add the following line to this file:

CYX SG 1 CYX SG 1 0.2 CYS2 CYS2