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Dear GROMACS Forum,
I am encountering issues with creating ligand topologies for my simulations. When I attempt to upload my ligands to generate parameters using CGENFF, I consistently receive errors. This issue occurs in most cases, and I have been unable to resolve it.
Additionally, I have used CHARMM-GUI to generate the ligand topology(using ligand reader and modeler) and included the itp in my topol.top file and the prm file in itp file of ligand( because whenever I included or did not included it in topol.top I got errors about improper dihedral) , but I am still facing errors when running the gmx grompp command. Here is the specific error message I receive:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
…
WARNING: Too few parameters on line of [unl.prm] (source file: toppush.cpp)
ERROR: Atoms in the .top are not numbered consecutively from 1
I have checked the generated topology and parameter files carefully, but I am still unable to resolve the warnings and the fatal error about atom numbering.
Could anyone provide guidance on how to fix this issue or recommend a troubleshooting step I might have missed?