# How to add an amide bond using Gromacs in Amber99sb-ildn ff

**URL:** <https://gromacs.bioexcel.eu/t/how-to-add-an-amide-bond-using-gromacs-in-amber99sb-ildn-ff/6211>\
**Category:** User discussions\
**Tags:** forcefield\
**Created:** [April 17, 2023, 9:45am UTC](https://gromacs.bioexcel.eu/t/how-to-add-an-amide-bond-using-gromacs-in-amber99sb-ildn-ff/6211 "2023-04-17T09:45:57Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![wu\_chic](https://avatars.discourse-cdn.com/v4/letter/w/f19dbf/32.png) [@wu\_chic](https://gromacs.bioexcel.eu/u/wu_chic)\
**Post date:** [April 17, 2023, 9:45am UTC](https://gromacs.bioexcel.eu/t/how-to-add-an-amide-bond-using-gromacs-in-amber99sb-ildn-ff/6211/1 "2023-04-17T09:45:58Z")

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GROMACS version:2022.3  
GROMACS modification: No  
Here post your question:  
my peptide sequence is: F-P-ORN-A-W-Y, I want the NE of the sidechain of ORN to form an amide bond with the C-terminus of the peptide.  
I add ‘Tyr C 1 Orn NE 1 0.136 Tyr Orn’ into the specbond.dat, after I ran gmx pdb2gmx in Amber99sb-ildn ff, the C-N bond was formed between OC2 and NE. However, additional atoms like OC1 of Tyr and HE1, HE2 and HE3 of Orn are also connected to the C-N bond. I checked the input pdb file there is O of Tyr exist, but no OC1, OC2, HE1, HE2 and HE3 exist.  
Could you please let me know what I did wrong and how to form a correct amide bond? Thank you very much.

Cheers,  
Wu