My aim is to simulate cnt with aminoacids(histidine) in water solution. I`ve made two separate topology files(15 molecules of histidine with pdb2gmx command and cnt topology with x2top) then merge them in text editor. I have an error "No default Proper Dih. types".
I assume "ffbonded.itp" file need to be completed with [dihedraltypes] parametrs. Is that correct? I used charmm27 ff, so how can i define these parametrs: func, phi0, cp, mult?
It would be greatly appreciated if someone will supply with correct methodology of crafting topology file for this situation.