Results analysis - water refinement -

Dear all,

I have a question regarding results after water refinement performed using Multi-body interface of Haddock2.2 and the following recipe:

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 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 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 ( indicate that something is wrong with the initial structure?

Thank you very much,

When the water refinement by MD fails (probably due to some bad geometries, Evdw clashes…), only a minimisation is performed and this give the same results for all models (which are identical from the start)

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Thank you very much for your fast reply and the explanation.