Check the answers to this question, they should still be valid:

https://www.researchgate.net/post/How-to-create-topology-file-for-new-ligand-in-gromacs

Thank you Annemarie Honegger !

Gromacs has tutorial about performing MD simulation for protein-ligand complex, it might help

http://www.mdtutorials.com/gmx/complex/index.html

Thank you Fedaa Ali !

Dear all,

I was able to generate the itp files for unnatural amino acids and the linker using ATB web server.

Can anyone suggest to me how to generate topology(.itp and .top) for the whole peptide chain ?