How to solve Fatal error: Topology include file "LIG.prm" not found in add ions step in gromacs?

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Nor Farrah Wahidah Ridzwan

Hi Muhammad Abdul Bari ,

Based on your statement, it appears Gromacs is expecting a "prm" file for the ligand's topology instead of an "itp" file.

You may want to double check the particulars of the force field you choose and its' relvant steps in handling ligands.

All the best.

Md. Al-Amin

The error message "Fatal error: Topology include file 'LIG.prm' not found" in GROMACS typically indicates that GROMACS is unable to locate the parameter (.prm) file for a ligand (LIG) during the addition of ions step. This error usually occurs when the topology file for the ligand is not specified or cannot be found in the working directory.

Here are some steps you can take to resolve this issue:

Check File Location:Ensure that the 'LIG.prm' file is present in the working directory where you are running GROMACS. If the file is not in the current directory, provide the correct path or copy the file to the current directory.

Specify Full Path in Topology File:If you have a separate topology file (.top), make sure the path to the ligand topology file is correctly specified within that file. Open the .top file and check if the 'LIG.prm' file is referenced with the correct path.

Check Naming Conventions:Ensure that the ligand parameter file is named exactly as expected by GROMACS and that the file extension is correct (.prm). GROMACS may be looking for a file with a specific name, and deviations from that naming convention can lead to this error.

Verify Topology File Contents:Check the contents of the ligand topology file ('LIG.prm'). Make sure it contains the necessary force field parameters and information for the ligand. If the file is incomplete or corrupted, GROMACS may not be able to read it properly.

Update Force Field Files:Make sure that the force field files needed for your ligand are correctly installed. Check that the force field files and parameters for the ligand are available in the GROMACS installation directory or in the directory specified by the GMXLIB environment variable.

Check GROMACS Version:Ensure that you are using a version of GROMACS that supports the force field and parameters used in your system. Different GROMACS versions may have different force field parameter requirements.

After checking and addressing these points, try running the GROMACS simulation again. If the issue persists, you may need to provide more specific information about your system setup, force field, and the contents of the topology and parameter files for further assistance.