Refinement starting at it1 stage?

HADDOCK
1

Hello,

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!

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2

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.

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Thank you very much for your help!