To use the model that mixes the BLOSUM50 and THOM2 scoring matrixes, you need to set the model type to 8 by modifying the line in the following manner:
@ USR_MODEL_TYPE                                    8
and to add the mixing value (customizable) by adding the line:
@ USR_MIXING_VALUE                                0.125

where the present value represent the weight put on the BLOSUM50 scoring, 0.0 representing pure threading with THOM2 potential.

All other parameters remains same as in the original LOOPP version. A template of the loopp.par file can be found in the zip package.