For example, there are many Brookhaven PDB files which do not correspond exactly to what LEaP expects. I solve this by checking which residues give extra atoms when I load the original PDB file, then resolving all problems using a copy of the original PDB file. Then 'tail xxx' to see the contents of leap's dying gasp. LEaP can't find some new atom types I added for my molecule. Building atom parameters.
Atoms have names and types.
The force field is essentially a definition of the properties of different atom types. If you add a new type, you must define it - this is normally done in a frcmod file. However, one does not want to add new atom types to the force field unless absolutely necessary, since it means also generating bond, angle, and torsion parameters for the new type. The best definition of atom types is probably the one on our web pages, since it was written specifically to be understandable at the undergrad level, with the help of Dr. Kollman. If you do have to generate new types, see parameter generation, which is also in the appendix of the manual.