The tr322 model was initially optimized in three ways
gromacs
repacking sidechains (except PRO and CYS) by rosetta
gromacs + repacking sidechains (except PRO and CYS) by rosetta
The four tr322 models were evaluated with undertaker and
tr322.gromacs0.repack-nonPC.pdb was chosen for further optimization.
The model was superimposed on 2fs2A and 2fs2B to make a dimer and all
subsequent optimizations were done in the dimer context.
Refinement consisted of rounds of
optimization with undertaker (with slightly different cost
functions each time)
optimization with gromacs
repacking of sidechains (except PRO and CYS) by rosetta
Refinement model 1 is try14-opt2, the best-scoring model with most of the
undertaker cost functions used. It has the smallest chain breaks.
Refinement model 2 is try9-opt2.unpack.gromacs0.repack-nonPC, the model
that rosetta likes best of all the ones it repacked.
Refinement model 2 is try13-opt2, the model that scores best with some
undertaker cost functions, and second best with most. It has the
densest local packing.
Refinement model 4 is try13-opt2.unpack.gromacs0.repack-nonPC, the model
that rosetta likes second best of all the ones it repacked.
Refinement model 5 is try8-opt2, an earlier version of model 2.
Although many of the undertaker runs started with multiple initial
model and allowed crossover, the following history traces the main
contributions to the models.
try14-opt2 < try13-opt2.unpack.gromacs0
try13-opt2 < try12-opt2 < try11-opt2.unpack.gromacs0
try11-opt2 < try10-opt2 < try7-opt2.unpack.gromacs0
try9-opt2 < try8-opt2.unpack.gromacs0
try8-opt2 < try7-opt2.unpack.gromacs0.repack-nonPC
try7-opt2 < try6-opt2.unpack.gromacs0
try6-opt2 < try5-opt2 < dimer-tr322-2fs2A