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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? Any help or insight would be greatly appreciated.
I have uploaded my topol.top, it file and prm file of my ligand
topol.txt (855 Bytes)
UNLitp.txt (17.4 KB)
unlprm.txt (11.4 KB)
Thank you in advance for your time and assistance!
Best regards,
Erfan