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

**URL:** <https://gromacs.bioexcel.eu/t/how-to-set-the-bond-constraint-of-the-sidechain-in-a-self-designed-peptide/11541>\
**Category:** User discussions\
**Tags:** pdb2gmx, topology\
**Created:** [February 13, 2025, 1:01pm UTC](https://gromacs.bioexcel.eu/t/how-to-set-the-bond-constraint-of-the-sidechain-in-a-self-designed-peptide/11541 "2025-02-13T13:01:31Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![Linqy](https://avatars.discourse-cdn.com/v4/letter/l/bbce88/32.png) [@Linqy](https://gromacs.bioexcel.eu/u/Linqy)\
**Post date:** [February 13, 2025, 1:01pm UTC](https://gromacs.bioexcel.eu/t/how-to-set-the-bond-constraint-of-the-sidechain-in-a-self-designed-peptide/11541/1 "2025-02-13T13:01:31Z")

</div>

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.

---

<div class="post-metadata">

**Author:** ![H.Mosaddeghi](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/h.mosaddeghi/32/4066_2.png) [@H.Mosaddeghi](https://gromacs.bioexcel.eu/u/H.Mosaddeghi)\
**Post date:** [February 14, 2025, 8:07pm UTC](https://gromacs.bioexcel.eu/t/how-to-set-the-bond-constraint-of-the-sidechain-in-a-self-designed-peptide/11541/2 "2025-02-14T20:07:19Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![Linqy](https://avatars.discourse-cdn.com/v4/letter/l/bbce88/32.png) [@Linqy](https://gromacs.bioexcel.eu/u/Linqy)\
**Post date:** [February 15, 2025, 9:54am UTC](https://gromacs.bioexcel.eu/t/how-to-set-the-bond-constraint-of-the-sidechain-in-a-self-designed-peptide/11541/3 "2025-02-15T09:54:23Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![Linqy](https://avatars.discourse-cdn.com/v4/letter/l/bbce88/32.png) [@Linqy](https://gromacs.bioexcel.eu/u/Linqy)\
**Post date:** [February 18, 2025, 5:57am UTC](https://gromacs.bioexcel.eu/t/how-to-set-the-bond-constraint-of-the-sidechain-in-a-self-designed-peptide/11541/4 "2025-02-18T05:57:18Z")

</div>

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.

 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/8/8a294dfbca68208c2036b6cb3dedac9b1d76e0ef.png)

The odd structure is showed as follows.

 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/a/a454dd290d4f7e4e3e67e288fb2d473722c0e482.png)

 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/0/0720e30d2a54ebcb47ae7f8b7fb04952c5271570.png)