Dear Priyanka Choudhary

Kindly try to check the coordinates of your ligand and Generate topology files using CGENFF or CHARMM-GUI!

After generating. str file from Cgenff

Run this script to install Python 3.5 as an error generates while generating ligand topology.

apt-get install python3.5

pip uninstall pip

wget https://bootstrap.pypa.io/pip/3.5/get-pip.py

python3.5 get-pip.py

pip -V

pip install numpy

pip install networkx==2.3

pwd

then run the script

python3.5 cgenff_charmm2gmx.py Ligand Ligand.mol2 Ligand.str charmm36-jul2022.ff