I am inquiring to see if it is possible to run refinement jobs starting at the it1 stage, instead of the water refinement stage. I would like to take a pre-docked complex, put it through semi-flexible refinement, and then into the explicit solvent refinement. There is a nice tutorial on how to run only water refinement in the
examples/refine-complexes directory (as well as the refinement interface on the web-server) but I have not seen anybody run refinement with the it1 stage. Is this possible to do?
Any suggestions and/or examples would be of great help. Thank you!