Hi. I am working on system which includes protein monomer, small molecule and 10 bp DNA. I want to refine my system, so I used HADDOCK 2.4 for this. But after the refinement, I saw that the C atom of the small molecule was not displayed. Related images are attached.
First I kept the small molecule and protein in the same chain. When I got this result, I defined the small molecule and protein as separate molecules in different chains. However, the result has not changed.
I am also adding my input and output files. What can be the problem?