Can I merge protein and ligand after pdb2gmx?

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1

GROMACS version:2021
GROMACS modification: No
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When I use protein-ligand as input to run pdb2gmx with -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 gro and top files to add the ligand. This works all right. But protein and ligand are treated as two different moleculetype.

Is there a way to make protein and ligand into one moleculetype?

2

Just to update, I now found the solution to this, i.e. create a index for protein-ligand complex.

http://www.mdtutorials.com/gmx/complex/06_equil.html