Dear Rosetta Community,
I am trying to test run RosettaDNA protocol. For some background of the test, please refer to my early post on the forum: http://www.rosettacommons.org/content/rosettadna-error
I have a question regarding to residues designed around DNA binding interface by multistate design. The protein-DNA binding example I used is zfn268. When studying the output models, I saw Rosetta mutated a few key arginine residues away. These Arg residues are very important to DNA binding affinity and specifically by forming favored interaction to DNA major groove. To get understood why these Arg are mutated, I studied the scoring results. One observation is that the reference energy term of Arg is very high (probably the highest among all 20 AA). I guess on the amino acid level, the high ref energy of Arg may be due to it's high degree of freedom. But in the DNA binding case, these Arg are very helpful for DNA binding. I would rather mutate some other residues to Arg instead of mutate Arg away.
The weight of reference energy is set at 1 by default in the RosettaScript. I wonder if there are easy way in RosettaScript to lower the weight of reference energy or just reparametrize ref energy of Arg to a lower value. Any other approaches are also welcome. Thank you for your help.