I'm running RosettaScripts with an Enzdes xml file taken from Fleishman et al PlosOne 2011 (file attached). I'm using Rosetta 3.5 wk52 release. It is working; however, because the enzyme design documentation is not written for rosettascripts, I'm confused as to which options I should include. In particular, my score file does not include many of the parameters (such as interface energies) mentioned in the documentation, and I wonder if this has something to do with the options I provide. I also wonder if this has to do with the talaria changes, but passing -restore_pre_talaris_2013_behavior is incompatible with my xml file.
Any suggestions? Should I stop using RosettaScripts or is there something I need to add to get a more complete score output?
Thank you in advance.