I want to convert the pdb format of topoisomerase I into Gromacs.The pdb id for the structure is 1K4T. I removed ligands, water and Hg ion from 1K4T. But DNA is required for the MD simulation.

I gave the following command,

pdb2gmx -f 1K4T.pdb -inter -p system.top -o 1K4T_new.pdb

 I used the "AMBER03 protein, nucleic AMBER94" as the fore field and SPC/E as the water model.

I got the following error.

Fatal error:

Residue 10 named DT of a molecule in the input file was mapped

to an entry in the topology database, but the atom O3' used in

that entry is not found in the input file. Perhaps your atom

and/or residue naming needs to be fixed.

Can anyone help me?

Thank you.