GROMACS version: 2018.3
GROMACS modification: No
I picked a binding site from Autodock simulation, and saved the ligand at that binding site as a PDB.
Then I added its content to a protein PDB file by copying and pasting. (i.e. I tried to create a PDB file for protein-ligand complex)
After that, I ran pdb2gmx, and I got error as follows:
Residue ‘LIG’ not found in residue topology database
It seems to be saying there is no data on the ligand in the forcefield.
How do I solve the problem? I think I will need a step-by-step help on it. I am using AMBER99SB-ILDN forcefield.