Perform refinement in batch/automatic mode after rescoring the complex from initial rigid-docking stage

HADDOCK
1

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin LabPreformatted text

Hi!

I am interested in refining docked models using SAXS curve. According to the new score function (include chi^2, the discrepancy between experimental SAXS curve and the back-calculated curve), the top models from rigid-docking (it0), will be selected for further refinement (semi-flexible docking). As demonstrated by the previous work using haddock (Acta Cryst. (2013). D69, 683–694), such treatment could improve docking performance or success rate, compared to just screening the final models against SAXS curve after docking. naively, I can turn off it1 docking option in the run.cns file, and only perform rigid-docking, then select best models using new score function. I would like to know how to perform refinement docking for hundreds selected models in batch mode. or is there any other alternative way to do that? Thank you!

Best regards

Zhhxu

2

One way of doing that would be to set the number of models to 0 for it1 and water.

Do the rescoring of the it0 models and then edit run.cns to define a number of models for it1/water and restart haddock.

As for batch mode, check:

https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-local-tutorial/#configuring-haddock

https://www.bonvinlab.org/software/haddock2.4/run/#parallels-jobs

3

Thank you for your suggestions.