I am modeling a cytochrome P450, I am able to include the heme in my
model. However, in the templates the heme iron is bound to a cys
residue, but I loose this bond in the model. How can I go about
keeping it in my model?
If you have a CYS residue in your model aligned with that template
residue, then Modeller should automatically keep that bond in your model
(see the third bullet point at
http://salilab.org/modeller/9v7/manual/node65.html). This does, however,
require Modeller 9v5 or later. The heuristic is a simple one though - if
the bond is longer than 2.3A you could just add a simple distance
restraint to approximate this interaction. But really to do this
properly you need to tell Modeller that that CYS residue is not really a
'CYS' but is a modified residue (i.e. that it has a bond to your iron).
For that you'd need to patch your topology using the model.patch()
command and some knowledge of how CHARMM patches work, which can be
gleaned from the CHARMM manual.