Error in topol.top and sol.gro files

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1

GROMACS version: 2022
GROMACS modification: Yes/No
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I am getting stuck at the add ions step in protein-ligand tutorial of groamcs where the error given:
atom name 1 in topol.top and solv.gro does not match (N - C2)
similar lines till 20 atoms
(more than 20 non-matching atom names)

(more than 20 non-matching atom names)

WARNING 1 [file topol.top, line 52]:
17838 non-matching atom names
atom names from topol.top will be used
atom names from solv.gro will be ignored
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
There were 3 notes

There was 1 warning

If you are sure all warnings are harmless, use the -maxwarn option.
How do I resolve this?

2

what is the molecule at line 52? you have different naming in topology and gro file. Add maxwarn 1 and use the names from topol.top

3

I will strongly advise against this. A mismatch in this case indicates a complete disagreement between the coordinates and topology and is not a trivial nomenclature issue like one might see with H atoms or some water models. The order of the atoms in the coordinate and topology files must be identical. Edit the coordinate file accordingly, or backtrack and use a set of coordinates that is consistent with the topology (it must have aligned at some point, or the topology wouldn’t have been written the way it was).

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4

ohh i see that…!!, my mistake, the mismatch was N-C2.