Heme b pdb file for docking

1

Hello all

I’m currently doing my master thesis and I wanted to perform the docking of heme b to a protein in order to get an idea on the docking site, but I’ve been having problems trying to get a working pdb file for the heme. The examples given on HADDOCK Web Server - Settings don’t seem to be working anymore, and the pdbs I’ve been using don’t allow me to change the charge of the iron, coming out with a topological error whenever I do so. My question is if it’s not possible to change the charge of the heme iron, or if it requires something other than just changing the pdb.

Thank you in advance,
Martim

2

Check https://rascar.science.uu.nl/haddock2.4/library for an example of how to define the metals in a PDB file

3

I have followed those examples, specifically this one for the heme iron.

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Can I change the charge of the iron on the pdb? Because the example given for ions is different.

HETATM 3833 ZN+2 ZN2 A 42 21.391 -8.794 33.944 1.00 24.37 ZN

Thank you,
Martim

4

The iron in the heme is part of the heme and not a standard ion in that respect. You should not change it.

For other ions you can indeed specify the charge state.