How to set the bond constraint of the sidechain in a self-designed peptide

[Linqy]

GROMACS version:2021.3-bioconda
GROMACS modification: Yes/No
Hello! I’m a big fan of GROMACS and recently I have been researching on a peptide of 30 amino acids which is designed by myself based on the published articles, then I predicted the structure of the peptide by alphafold2 and it seems like what I want. However, a amide bond that I want to be formed between the Lys18 and Glu22 amino acid wasn’t observed in the .pdb file from the alphafold2 export .pdb file. Now I hope to add the bond to the structure when I anaylze the molecular dynamics simulations by GROMACS, but in the past 1 month when I self-learned GROMACS, I didn’t get the method to realize my ideas and stuck in the dilemma for a period of time. So I turn to You and hope to get some instructions here. I would appreciate it if you give me some advice.

[H.Mosaddeghi]

if possible for you, please share with me, your structure file then i check it.

[Linqy]

Thank you! I would like to. But I am not sure what the structure file meas, is it the pdb file？

[Linqy]

Hello! I have finished a MD simulation, but the peptide runs strange. Could you please help me have a look at my figures? Thank you very much!!!
My primitive peptide structure is like this.

The odd structure is showed as follows.