FATAL ERROR : neutralizing system

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I am getting this error when trying to use grompp for adding ions to neutral the system. I am not sure what am I doing wrong?

Fatal error:
Syntax error - File charmm36.itp, line15
Last line read:
‘1 2 yes 1.0 1.0’
Found a second defaults directive.

charmm36.itp is a file from CHARMM-GUI, and includes only a subset of the system. Here it appears it is a ligand? What CHARMM-GUI gives you is designed to be a standalone topology and can sometimes be hard to modify. Here, it’s a very simple matter of removing the [defaults] directive from charmm36.itp but be advised that you may encounter issues with redefined parameters as a result of trying to do this, because you’re essentially repeating (or replacing) much of the force field in the [*types] directives.

The better approach is to simply generate a topology for the ligand using the CGenFF server and convert it to GROMACS format, e.g. by following Protein-Ligand Complex

Hello Dr. Lemkul,

Thank you for the response. I tried generating the ligand from CGennF but somehow my ligand is getting squished


Your coordinate file is incorrectly formatted, perhaps from a residue name that is too long and caused a column shift in a PDB file.

Hello Dr. Lemkul,
Thank you for the suggestion, yes, it was the long residue name. I am having another error in the next step when I am trying to neutralize my system using your instructions from the tutorial.

Hello Dr. Lemkul,

Can you please provide suggestions to the below mentioned error.

Follow the tutorial more closely. The location of the #include statement for the ligand parameter file is crucial to get right, and the tutorial specifically discusses this.

Hello, Dr. Lemkul thank you for the reply. It seems like the problem still persisted. I have also referred to the link Errors - Gromacs

but still cannot add ions. getting the same error
Fatal error:
Syntax error - File tri.prm, line 2
Last line read"
Invalid order for directive bond types

All I can do is repeat what I said above. You can’t include new parameters after you’ve started defining molecules. The tutorial tells you exactly where you need to place the #include statement when dealing with ligand .prm files.

Thank you for your suggestions Dr. Lemkul. I am able to solve the issue now.