Fatal error: Residue 'EDO' not found in residue topology database

User discussions
1

GROMACS version:2023
GROMACS modification: Yes
Here post your question

Program: gmx pdb2gmx, version 2023
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 616)

Fatal error:
Residue ‘EDO’ not found in residue topology database

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
Please, someone to guide me . I am having this error.

2

Did you visit the link provided in the error message? Or perhaps Google for an answer? You may just find a huge number of useful forum posts :)

3

Yes. I google it out but I couldn’t find a precise answer to this problem in particular.

4

You won’t find an exact solution for your exact residue. But the answer is always the same in every post you will find - pdb2gmx can only handle species that already exist in force field .rtp files. It’s not magic. If you have a nonstandard species, you have to parametrize it yourself or use external (non-GROMACS) programs to write a topology.