Fatal error: There were 2 errors in input file(s) during ionization by using grompp module

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                 :-) GROMACS - gmx grompp, 2023.2 (-:

Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/drr-18/Documents/3ERT/4d17
Command line:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

Ignoring obsolete mdp entry ‘title’
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 503307263

Generated 167799 of the 167910 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1

Generated 117432 of the 167910 1-4 parameter combinations

ERROR 1 [file unl.itp, line 556]:
Duplicate atom index (21) in virtual_sites3

ERROR 2 [file unl.itp, line 557]:
Duplicate atom index (25) in virtual_sites3

Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’

Excluding 3 bonded neighbours molecule type ‘UNL’

Excluding 2 bonded neighbours molecule type ‘SOL’

NOTE 2 [file topol.top, line 40057]:
System has non-zero total charge: -3.000000
Total charge should normally be an integer. See
Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation
for discussion on how close it should be to an integer.

Cleaning up constraints and constant bonded interactions with virtual sites

There were 2 NOTEs

Program: gmx grompp, version 2023.2
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2198)

Fatal error:
There were 2 errors in input file(s)

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

2

The error says that there are errors on lines 556 and 557 in unl.itp. Start looking there.

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