[gmx-users] Protein-Peptide Simulation help

[Syed Azeem]

Hello All,

I'm trying to simulate a Protein-Peptide complex using GROMACS 5.1.4.
For reference, I referred Justin Lemkul's Tutorial for Protein Ligand
complexes. In which, the topology for ligand (small molecule) was
generated using PRODRG.

In my case, do I need to treat my peptide (16-mer) in such a way? Or
just directly simulating the protein-peptide complex is good enough?

Thanks in advance

Azeem