# Docking for mutated peptide

**URL:** <https://ask.bioexcel.eu/t/docking-for-mutated-peptide/6002>\
**Category:** HADDOCK\
**Created:** [February 10, 2026, 9:47am UTC](https://ask.bioexcel.eu/t/docking-for-mutated-peptide/6002 "2026-02-10T09:47:05Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![needhelp](https://avatars.discourse-cdn.com/v4/letter/n/fbc32d/32.png) [@needhelp](https://ask.bioexcel.eu/u/needhelp)\
**Post date:** [February 10, 2026, 9:47am UTC](https://ask.bioexcel.eu/t/docking-for-mutated-peptide/6002/1 "2026-02-10T09:47:05Z")

</div>

Hello!

I have an ongoing project. I have a peptide with 8 residue and this specific conformation is from a MD. Now I want to mutate the peptide with a nonstandrad residue (NSR). For example I want to mutate Phe6 to Cha (cyclohexylalanine) while keeping the other residues intact (the mutated residue is in the middle). Regarding this I have question. I know you need a topology files for the nonstandard amino acids. I want to ask about.

1. The .top and .par you need is only for the non standard residue even it is in the middle of the peptide?
2. If I want to generate a topology file, what pdb should I use in acpype?

- Can I draw the NSR in visualization software and generate a topology file from here?
- can I use the topology file from atb website and no further editing needed? or
- i must get the details and teh pdb from the mutated peptide by truncating the peptide and leaving only the NSR then subject it to acypype?

1. if i have topology and parameter files, do i need to align exactly the atoms names in the mutated peptide to work? if yes, does this mean that it should have N, CA atoms and I can’t use my drawn residue since it is standalone and not connected to other molecule?

Hoping someone can answer this. Thank you so much!