You must determine new parameters for yourself. The atom types you use in your new residue may be undefined in the force field and/or may be in new combinations of bonds, angles, or dihedrals. Studying the parameters for analogous situations may help in the determination of new parameters. There is a section in Chap. 12 of the Amber 8 Users' Manual (in the Appendix in earlier releases) on generating parameters. Also see the topics under "Parameters and representations..." in Questions and problems?
Similarly in leap.
We didn't create any new residues.
If adding crystallographic waters, see water. If your missing parameters involve Sulfur, e.g. ``Missing bond parameter: SH-SH (atoms 52- 566)'' you probably need to use the CYX residue for cross-linked CYS residues.
Missing mass parameter: Atom number 12 type LP Missing mass parameter: Atom number 13 type LP
You also need to switch to db94.dat at the Link stage. The parm94.dat params are to be used exclusively with this Prep dbase since the atom types are different in the new force field.