Reply To: a trouble during floppytail modeling

[Anonymous]

Binding energy is calculated in the function “create_extra_output” at the top of FloppyTail.cc. You may recall commenting out a function call to use FloppyTail, because some of its code is hard-coded for the original system in the Cell paper. That is the code you have to comment out, but it is also the code that calculated the binding energy you want.

If you know any C++, feel free to rewrite the contents of that function so that it applies to your system. That is how it was intended to be used. I forget what your model looks like, but basically you can create Poses from the pieces of the interaction you want and score them; then to get binding energy just subtract the total scores of the two halves of the interface from the total score of the complex: AB – A – B = AB binding energy.

By the time 3.3 rolls around, InterfaceAnalyzer will be released, which does a lot of stuff like this in a much simpler fashion.