A Generalised workflow for obtaining protein and peptide molecular structures, docking the peptide into the protein and running a molecular dynamic simulation over a large number of trajectories.
Then LEaP is able to read all of the nisin molecule (```gfp.pdb```) and will create the corresponding topology (```gfp.prmtop```) and coordinate files (```gfp.prmcrd```). When this happens LEaP will output the following onto the screen
You probably don't need the additional "frcmod" file. Better check your atom types in your "ac"-file as they are typically wrong for new non-standard amino acids. For example the amide N atom often has the type "NT" and will be non-planar.