# Protein-peptide ligand MD

**URL:** https://ask.bioexcel.eu/t/protein-peptide-ligand-md/3952
**Category:** MDWeb
**Created:** [October 20, 2022, 3:54pm UTC](https://ask.bioexcel.eu/t/protein-peptide-ligand-md/3952 "2022-10-20T15:54:54Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![DimChem13](https://avatars.discourse-cdn.com/v4/letter/d/bbce88/32.png) [@DimChem13](https://ask.bioexcel.eu/u/DimChem13)
#### Post date: [October 20, 2022, 3:54pm UTC](https://ask.bioexcel.eu/t/protein-peptide-ligand-md/3952/1 "2022-10-20T15:54:54Z")

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Hello,

I would like to perform MD of a peptide ligand with a protein using MDWeb but I am a bit confused on some step and I would like to kindly ask for some help.  
If the pdb file of the protein I want to use only exist as bound to another ligand (no apo), can I still use it? Do I just select remove it at the stage when I am checking the protein (when it gives errors and warnings)?  
Regarding the ligand I want to use in my simulations, how and when do I include it? Do I need to prepare it somehow (it is a peptide)? It has been crystallized with another protein so can I save the ligand (e.g. in pymol; open the structure and save the ligand as pdb?) and include it in the MDWeb somehow?

I would appreciate any help.

Thank you so much.

All the best