Error Query Regarding pdb2gmx Generating TOP Files Containing DNA Fragments

User discussions
1

GROMACS version:2025.2
GROMACS modification: No
I am currently attempting to perform molecular simulations on a single-stranded DNA segment and a protein. First, I used ZDock to dock the DNA and protein together. Next, I used gmx pdb2gmx to generate the corresponding top file, but encountered the following error:
Program: gmx pdb2gmx, version 2025.2
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1087)

Fatal error:
There is a dangling bond at at least one of the terminal ends and the force
field does not provide terminal entries or files. Fix your terminal residues
so that they match the residue database (.rtp) entries, or provide terminal
database entries (.tdb).

The force field file I am currently using is amber14sb_OL15.ff, which was downloaded from User contributions — GROMACS webpage https://www.gromacs.org documentation

2

This is quite a generic error saying that pdb2gmx interprets one of your terminal residues as non-standard (could be either protein or DNA), next to impossible to guess what is wrong without knowing more about the structure. Are all your residue names standard, do you have a 5’ phosphate, are the separate molecules defined as different chains, did ZDock modify any of the standard PDB naming?

If these questions don’t raise any flags, feel free to share a sample PDB.