I'm trying to run MD simulations on GROMACS 2019.2 using CHARMM36m forcefield of pdb file 1MRQ, an enzyme complexed with NADP+ and 20alpha-hydroxyprogesterone.

I tried to parametrize the entire complex using the PDB reader tool provided by CHARMM-GUI, but it failed for both ligands, even though NADP+ (named NAP) is present in toppar_all36_na_nad_ppi.str file.

Therefore I used cgenff to get .str file for both ligands individually and converted them using cgenff_charmm2gmx but now I don't know exactly how to include those files to generate the correct .gro file using "gmx pdb2gmx".

I would like also to compare results obtained with a different forcefield, is there any fast and reliable tool to obtain parameters for another forcefield directly from the pdb file?

Any help or suggestion would be highly appreciated.

Thanks,

Valerio