# Protein peptide simulation **URL:** \ **Category:** User discussions\ **Created:** [April 10, 2025, 5:44am UTC](https://gromacs.bioexcel.eu/t/protein-peptide-simulation/11904 "2025-04-10T05:44:47Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![Harshaya](https://avatars.discourse-cdn.com/v4/letter/h/bc79bd/32.png) [@Harshaya](https://gromacs.bioexcel.eu/u/Harshaya)\ **Post date:** [April 10, 2025, 5:44am UTC](https://gromacs.bioexcel.eu/t/protein-peptide-simulation/11904/1 "2025-04-10T05:44:47Z")
GROMACS version: GROMACS modification: Yes/No Here post your question may i know how to seperate the protein and petide from complex.pdb file which is docked pdb file of proteina and peptide…i dont know how to differentiate the proteina and peptide …can any say how to seperate the protein and peptide from complex pdb file to generate a topology file? ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [August 12, 2025, 6:36am UTC](https://gromacs.bioexcel.eu/t/protein-peptide-simulation/11904/2 "2025-08-12T06:36:15Z")
By ‘differentiate the protein and peptide‘, are you asking how to create a new coordinate file for each one? Most straightforward way would be to open the pdb in a text editor and copy-paste the coordinates into their own pdb files. You could also use something like pyMOL to select a specific chain and export it as its own pdb. ---
**Author:** ![slovas](https://avatars.discourse-cdn.com/v4/letter/s/e274bd/32.png) [@slovas](https://gromacs.bioexcel.eu/u/slovas)\ **Post date:** [August 12, 2025, 2:38pm UTC](https://gromacs.bioexcel.eu/t/protein-peptide-simulation/11904/3 "2025-08-12T14:38:11Z")
create an index file that has two new groups, let’s say chain\_A: protein and chain\_B: peptide you can also convert your gro file to pdb format in which you can have chain designations