GROMACS modification: No
Here post your question
When I use protein-ligand as input to run
-merge all option, the protein and ligand can be merged into one molecule but causes errors because the ligand atoms are not found in the residue topology database, which makes sense.
So I use protein only to run
pdb2gmx, then manually modify the protein
top files to add the ligand. This works all right. But protein and ligand are treated as two different
Is there a way to make protein and ligand into one