I am trying to use HADDOCK to dock a Ligand (NADH) with a protein that contains a FAD cofactor, but when I submit the job the run always fails. Is there a way for this program to recognize the FAD as a protein cofactor?
Thanks in advance
Should work in principle - your FAD should be defined as HETATM.
The question is why is your run failing. Please share a link to your result page
https://wenmr.science.uu.nl/haddock2.4/run/3778211238/294935-SIP_FAD_NADH
In this run I identified the cofactor as FAD. In the first run I identified it as UNL.
Thank you
Deleting all hydrogens from your FAD prior to submission makes it work. But then you get the next error that no restraints were defined…
Thank you for the input. I will try to fix that.