Is it possible to accurately simulate the effect of ligands on protein-DNA complex

User discussions
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GROMACS version:feb2023
GROMACS modification: Yes, GPU acceleration

I am using the Charm36 forcefield to try and simulate a protein-ligand-dna complex generated using docking but keep receiving errors when using pdb2gmx such as "Atom C7 in residue DT 4 was not found in rtp entry DT with 32 atoms while sorting atoms. " I have assigned using -ter to assign protein end and 5ter and 3ter ends of DNA. How else should I edit the pdb/add to the rtp file to make this compatible with Charm36? Thanks in advance for any advice you can give.

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pdb2gmx is complaining about the naming of the methyl group in DT. CHARMM expects these to be named C5M but many PDB files have them listed as C7. Update the names in the PDB file and it should work fine.