Thanks very much!
It seemed I`ve handled this trouble following your great suggestions. One thing required to confirm was whether the donor or acceptor in atom_properties file meant donor or acceptor of electrons?
Actually, in my case, although Ca ions were not included in floppytail region, it served to stablized an acid region. Based on my previous practical running of FloppyTail, if there was no Ca ion, basic parts of floppytail models with lowest energies would fall into that region. So I wonder whether there could other possible conformations, except for hanging around that acid region. Also, I checked the supplement information of your Cell paper, and it said models would be evaluated by scorefunction which took into account electrostatics and other energies in centriod phase.
So you meant scorefunction could not treat positive charges of Ca well ?