Heme docking/ data preparation for HADDOCK

HADDOCK
1

Hi all,
I just started to work with HADDOCK and have a general question. I want to dock a protein with a heme b to another protein. For that as far as I understood I need to rename the residue HEM to HEB in the PyMol/ .pdb file and in the topology file I need to name the HEB and FE from HETATM to ATOM so that HADDOCK can proccess the data.
I am not sure how to do this and would be thankful if you can help me please.

  • can I use the alter command, if yes, how?
  • or ii also tried to open the file in editor, do the changes but then I have a .txt file that i cannot use anymore as I need a .pdb file for HADDOCK.
    Thank you for helping me!
2

Check: https://milou.science.uu.nl/services/HADDOCK2.2/library.html

The bottom of that page provide links to example PDB files.

When editing your files, make sure to use a simplex ASCII text editor and save the file as ASCII text with .pdb as extension.