Hello! I ran my WT protein in HADOOCK2.4 and wants to know the effect of modifying the lysines into different methylation status in the complex structure. So, after docking the WT, I changed the names of the LYS in my pdb to MLZ or MLY and ran the refinement. However, after the refinement, I noticed that no charge was assigned for the modified lysines. Does this affect the refinement result and how do I fix it?
Dear user,
Charges are not present in the PDB file themselves, but rather in the force-field that we used.
If you can observe the proper methylation state on your modified Lysines, they should be taken into account during the computation and therefore the related force-field parameters used accordingly.
If that is the case, the results are probably correct.