Refinement (it1) of a selected structure from it0 stage

Hello all,

I would like to know how I can perform it1 stage refinement of a selected structure(s) obtained from it0 docking. The structure is not the lowest energy pose as per it0 scoring function. I am guessing this is not possible?

I have performed docking up to it0 stage for a huge number of protein-protein complexes, by setting structures_1=0 which will prevent further docking steps. I am aware that I can separately start it1 after it0 runs are complete by modifying the run.cns file (ie editing structure_1=x). The problem is that the lowest scored ‘x’ poses are automatically refined in it1. But I am not happy with the weights of the terms used in it0’s scoring function, so I have re-scored the poses based on my custom weights. This will naturally result in a different ranking of the poses from what is expected from the default scoring function used in it0. Now, I would like to know how I can refine the top ‘x’ structures based on the custom scoring function that I have used. (Note that the reweighted scores and names of the pdbs are in a new file called rescored.txt)

Feel free to message for additional clarity. Thanks in advance for your help.


Simple edit the file.nam, file.cns and file.list files to have the files you want to refine in those, specify the number of models you want to refine in run.cns (structures_1) and restart HADDOCK

Thank you @amjjbonvin, it has worked!