Modeller uses CHARMM format topology and parameter files, and includes CHARMM 22 parameters for all standard amino acids, as well as some common ligands. For ligands not covered in these files, you can either treat them as rigid bodies or define parameters and topology for them.

In the latter case, you can use this page to add your own parameter and topology files for others to use, or browse those other users have submitted. Anybody can edit these pages (although you must login first).

Other useful links