GROMACS version: 2023.3
GROMACS modification: Yes/No
Here post your question ’
I’m trying to perform MD simulation for viral protein-ligand complex. I plan to use CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) for the viral protein and then CHARMM all-atom force field for the small drug-like compound.
I encountered a fatal error (atom C1 not found in buiding block 1MET while combining tdb and rtp) when using CHARMM all-atom force field for the protein. -ter and -ignh do not work, nothing I do works. However, it ran perfectly when I used CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
I will assign ligand topology to the small drug-like mol.
Would the result be affected or is it alright to proceed?