I'm trying to use rosetta to compute changes in free energy of binding of a protein-protein complex upon mutation from wildtype.
On using the options listed at [http://www.rosettacommons.org/tiki/tiki-index.php?page=Commands+Tutorial...|Commands Tutorial] along with the -mutlist option, my output (INT_OUT file) contains ddg_binding values for each of the mutations I listed. However, the contribution of the dunbrack energy to the ddg value is always zero.
Does this mean that the side chains are not minimized upon mutation?
I changed the interface weights in weights_manager.cc so that Wdun was non zero(I set it to 1), but the output still has dun energy to be zero. Is there some other reason the energies are zero? I have tried other variants in the input options including setting -repack, -softrep.
If the default behavior is not to minimize the side chains, is there any flag I can set to enable it? Also, If there is a set of recommended flags to enable while computing ddgs, that is different from the tiki page mentioned above, could someone please point me to it?