# Not able to create disulfide bond using -ss command with pdb2gmx

**URL:** <https://gromacs.bioexcel.eu/t/not-able-to-create-disulfide-bond-using-ss-command-with-pdb2gmx/7035>\
**Category:** User discussions\
**Created:** [August 17, 2023, 6:51pm UTC](https://gromacs.bioexcel.eu/t/not-able-to-create-disulfide-bond-using-ss-command-with-pdb2gmx/7035 "2023-08-17T18:51:49Z")\
**Posts on this page:** 1\
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**Author:** ![harpreetsingh05](https://avatars.discourse-cdn.com/v4/letter/h/77aa72/32.png) [@harpreetsingh05](https://gromacs.bioexcel.eu/u/harpreetsingh05)\
**Post date:** [August 17, 2023, 6:51pm UTC](https://gromacs.bioexcel.eu/t/not-able-to-create-disulfide-bond-using-ss-command-with-pdb2gmx/7035/1 "2023-08-17T18:51:49Z")

</div>

GROMACS version: 2018.1  
GROMACS modification: Yes/No  
I a trying to create disulfide bond between the two cysteine residues in my protein.  
I used the following command:-  
gmx pdb2gmx -f wt.pdb -o wt.gro -p wt.top -ignh -ss -merge all

This distance between the bonds is 0.202nm.  
However, I am not able to see the formation of disulfide bonds in the structure file (wt.gro) as well as the topology file (wt.top)

The files can be assessed at the following G Drive link:-  
[https://drive.google.com/drive/folders/1SAFYH-q59qLHwUUdz0XPsbWUbmc2YeTZ?usp=sharing](https://drive.google.com/drive/folders/1SAFYH-q59qLHwUUdz0XPsbWUbmc2YeTZ?usp=sharing)

I will appreciate any help in this regard.

Thanks in Advance