Refinement starting at it1 stage?


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!

Hi Jacob

You can indeed do that. In that case don’t set the number of steps for the it1 stages to 0 - leave those to the default values

And you can use either centre of mass of surface contact restraints. The remaining settings are the same as for the refinement examples.

Thank you very much for your help!