Usage: RESNAME drug.mol2 drug.str charmm36.ff h

User discussions
1

GROMACS version: 2020.1-Ubuntu-2020.1-1
GROMACS modification: Yes/No

Where am I going wrong in ligand topology?

hindol@hindol_cha:/mnt/c/Users/hindo/Desktop/MD Simulation/Final$ python cgenff_charmm2gmx_py2.py JZ4_mol2_fix.mol2 JZ4.str charmm36-jul2022.ff
Usage: RESNAME drug.mol2 drug.str charmm36.ff

2

Hi,
you are missing the residue name (short form: resname) of your ligand. It must be written after the name of the script “cgenff_charmm2gmx_py2.py” and before “JZ4_mol2_fix.mol2”.

Best,
Marius