I have a question regarding results after water refinement performed using Multi-body interface of Haddock2.2 and the following recipe: https://www.bonvinlab.org/software/haddock2.2/tips/advanced_refinement/.
Recently I got results for several structure-refinements where standard deviations for all energy terms were 0.0.
I have checked the folder …/structures/it1/water where for all 20 structures (Number of structures for the explicit solvent refinement = 20) there are files called complex_nw.fail and all 20 structures (complex_nw.pdb) are identical. Also all 4 cluster1_n.pdb are identical.
I would like to add that most part of the submitted structures could be refined and the differences between for refinement submitted structures are just in one point-mutation per structure. Although, I have noticed that most of the runs still have complex_nw.fail file for some of the structures.
I would like to ask what can be the reason for the failed water refinements, does it make sense to resubmit the jobs where all of the refinements failed or the presence of the failed structures (complex_nw.fail) indicate that something is wrong with the initial structure?
Thank you very much,