General force-field setup operations are performed using the "Energy" command of the "Compute" menu. These operations affect all molecular mechanics energy calculations performed throughout SYBYL during a given session. Setup operations can also be performed prior to energy minimization, but are reset upon exiting the minimization facility.
The quantities used for molecular mechanics calculations are taken from the molecule description of each structure in SYBYL's molecule areas, together with force-field parameters provided with the software. It is of particular importance that atom type codes be correctly assigned to all atoms because this information is used to access force-field parameters.