Error message

GROMACS version:2021
GROMACS modification: Yes/No
Here post your question I have an error message and I am trying to solve it but I couldn’t. The message is the receptor_ligand_solv.gro file number doesn’t match with my file. The file has more number. Could you please tell me how I can fixed this step to reach to ion.tpr file.

can you post more information on the the error you got?
I guess you get the error while you run gmx grompp and the error is about the number of atoms in the gro file does not match the number of atoms in the top file. If it is the case you can check that system defined in the topology file match the one in the gro file, by looking
if the list of the molecules in your system (at the end of the topology file) match the number of the atoms in the gro?


Hi Dr. Alevilla,
I still can’t figure out the problem. I will attach the error message and the f and ligand.itp file. Hopefully you can figure it out.
The command is gmx grompp -f ions.mdp -c protein_ligand_solv.gro -p -o ions.tpr
and the error message is WARNING 17 [file, line 42]:
Atomtype H4 was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn. (833.6 KB)