@jalemkul After removing only those quadruplets from the lig.prm which have also been defined in the ffbonded.itp, I could move past this hurdle.
But another anomaly creeped in during the energy minimization step. I had faced this earlier too while using the Jul-2021 version of charmm36.
@Mikel led me to another similar issue. I tried reducing the em_step size, increase the box dimensions but in vain. I’m still trying out other ways to work around this issue.