Reply To: Docking an iron atom to a peptide

[Anonymous]

We are wayyyy out into “wild guess” territory here.

The modification to the fasta will probably work if FE is the full residue type name for the iron atom. That name will appear near the top of the params file (you did find that, right? It looks like FE to me in my copy of the database).

For the constraint files, you’ll want to replace the ZN atom names with FE atom names. The cysteine SG’s will have the same atom names. You will need to replace all the residue numbers as well if your protein has a different number of residues. The constraint file documentation (http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/constraints.html) is frankly some of our best; if you can’t figure it out from this let me know. You will also need to fix the geometry of the constraints, if a tetra-cysteine iron does not have the same geometry as a zinc. It may be easiest to draw a picture of what the current constraints say then figure out what to tweak.