Dear All,
I have a peptide having the following synthetic amino acid, that needs to simulate using Gromacs. I have selected CHARMM36 force field and the initial topology for the synthetic amino acid has been generated using CHARMM-GPU.
I have modified the forcefield files acordingly. (.rtp and .hdb) .
Can anyone suggest to me how to modify ffbonded.itp and ffnonbonded.itp files?