Hello everyone, I hope you are doing great.

I am working with a protein homology model (Swiss Model) that I made using an experimental structure as template. The issue is that the experimental model has a DNA ligand, after I mutated that DNA structure with my own sequence I sent the homology model to YASARA Force Field Minimization Server. After getting the .sce data, saving the "End" as ".PDB"in YASARA Viewer and removing waters (Phenix), I found that atoms from the nucleotides backbones are missing at the time I used CCP4mg to evaluate the interactions of the ligand with the proetin... I've tryed sending my model again but the issue keeps appearing, does anyone know what can I do to solve this?

Thanks in advance!