I am trying to do protein-ligand complex md and am receiving the errors above. I have generated the ligand .itp files in the charmm-gui, I have the charmm.itp file that has the defaults in, but when i include both those itp files it says I can’t have two default files. however when I don’t have it it says I have no defaults. Any help would be greatly appreciated
Which molecules are defined in charmm.itp? In my experience, CHARMM-GUI usually outputs the forcefield.itp which has the defaults, itp files for the other individual molecule types and a topol.top that calls each of those itp files in the correct order.
How are you including the itp files in your topol.top and commands?