No Default U-B Types Error fix

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1

GROMACS version: 2024.2-Homebrew
GROMACS modification: Yes/No
Here post your question
I keep getting this error does anyone know how to fix this without doing it manually as it is thousands of lines:
gmx grompp -f ions.mdp -c npm_solvated.gro -p topol.top -o ions.tpr

             :-) GROMACS - gmx grompp, 2024.2-Homebrew (-:

Executable: /usr/local/bin/…/Cellar/gromacs/2024.2/bin/gmx
Data prefix: /usr/local/bin/…/Cellar/gromacs/2024.2
Working dir: /Users/jegankarunakaran/ScienceFair
Command line:
gmx grompp -f ions.mdp -c npm_solvated.gro -p topol.top -o ions.tpr

Ignoring obsolete mdp entry ‘ns_type’

NOTE 1 [file ions.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.

Setting the LD random seed to -173161667

Generated 20503 of the 20503 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1

Generated 17396 of the 20503 1-4 parameter combinations

ERROR 1 [file topol.top, line 1837864]:
No default U-B types

ERROR 2 [file topol.top, line 1837865]:
No default U-B types

ERROR 3 [file topol.top, line 1837867]:
No default U-B types

ERROR 4 [file topol.top, line 1837868]:
No default U-B types

… (There are a lot more lines)

ERROR 222654 [file topol.top, line 2171843]:
No default U-B types

ERROR 222655 [file topol.top, line 2171845]:
No default U-B types

ERROR 222656 [file topol.top, line 2171846]:
No default U-B types

ERROR 222657 [file topol.top, line 2171848]:
No default U-B types

ERROR 222658 [file topol.top, line 2171849]:
No default U-B types

ERROR 222659 [file topol.top, line 2609913]:
Unknown cmap torsion between atoms 32197 32199 32201 32219 32222

There was 1 NOTE

Program: gmx grompp, version 2024.2-Homebrew
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1713)

Fatal error:
There were 222659 errors in input file(s)

For more information and tips for troubleshooting, please check the GROMACS
website at Common errors when using GROMACS - GROMACS 2024.2 documentation

2

I don’t know how you generated your topol.top file, but my guess is that the force field parameters are not included there. Usually there is an #include close to the top of the topol.top file that includes force field .itp files.

3

Thank you so much I was able to fix it.