Question about Changing DNA residues to Protein in residuetypes.dat for covalent bond

User discussions
1

Hello,

I need to create a covalent bond between DNA and a protein in my system. To avoid this error in gmx pdb2gmx step:

((Residue DT24 in chain has different type (‘DNA’) from residue ASP2 (‘Protein’)…))

I changed DT/DA/DC/DG from DNA to Protein in residuetypes.dat, and minimization ran without errors.
Is this modification safe, or could it cause issues later in the simulation?

Thank you for your help.

Best regards,

Fatemeh,

2

@hess @jalemkul

Hello,
I have a single strand of DNA where both ends are modified nucleotides (named TO5 and TO3), and each of them is covalently bonded to a peptide.

The sequence looks like this:

TO5 (modified nucleotide, covalently bonded to peptide, marked as Protein in residuetype.dat)
→ peptide → TER → 21 standard DNA base pairs →TO3 (modified nucleotide, covalently bonded to peptide, marked as Protein in residuetype.dat)→ peptide → TER
I set both TO5 and TO3 as Protein in the residuetype.dat file so that GROMACS treats them and the attached peptides as part of one chain.

I also added the following lines to the specbond.dat file:

TO5 C 1 ASP N 1 0.130 TO5 ASP
TO3 C 1 ASP N 1 0.130 TO3 ASP
TO5 O3’ 1 DT P 1 0.160 TO5 DT
TO3 P 1 DC O3’ 1 0.160 TO3 DC

I have 21 standard DNA base pairs in the middle of my structure. They are not terminal, but GROMACS still asks me to select terminal patches during pdb2gmx. I tried selecting “None” for both the 5’ and 3’ ends, but GROMACS still gives an error and does not generate the topology.

Fatal error:
There is a dangling bond at at least one of the terminal ends. Fix your
coordinate file, add a new terminal database entry (.tdb), or select the
proper existing terminal entry.

For more information and tips for troubleshooting, please check the GROMACS
website at Common errors when using GROMACS - GROMACS 2025.2 documentation

How can I tell GROMACS to treat these residues as internal, so it doesn’t ask for terminal patches?

If I rename DT/DC/DG/DA as Protein in the residuetype.dat file, the sequence will be:

TO5 → peptide → 21 base pairs → TO3 → TER,
and I don’t get any errors, even after minimization.

I used the CHARMM36 force field. I want to make sure I’m not missing anything important and that this approach is acceptable.

Any advice would be really appreciated, and I really appreciate any help you can provide.
Best regards,
Fatemeh,