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.