I'm new here, and I have read the mannual of the RosettaDock on site
We want to do a Ab_Ag dock with your RosettaDock++ software. And we have read all the turouials of the software at http://graylab.jhu.edu/~mdaily/tutorial/index.html.
But we have no idea on how to write the FLAGS file to reach our aim. The detail informaiton is:
1. we want to improve the initial antibody's affinity by the method of mutation of some key or critical residues;
2. Initial Antibody-Antigen complex with high resolution is available, that to say, amino acid residues wihch are involved in interface are determined;
Can we do the following work with RosettaDock?
do some mutation, for example, we change Phe92to Ala92, can we comapre the binding affinity between the two antibodies(initial antibody and antiboy after muation) with the same antigen?
if the answer is yes, and how to do it with rosettadock?
if no, then can you give us some advice?
In addition, who can pass us an step by step tutorial about how to make antibody-antigen docking with RosettaDock?
Thank you very much!
The two sets of documentation you linked to are for different versions of RosettaDock. One version, which is part of Rosetta++ (or Rosetta 2.x), is the older version. The newer version is part of Rosetta 3.x. Which version are you trying to use?
we want to use the newer version RosettaDock?